Quality Control and Differential Gene Expression Analysis, Candida glabrata
Weronika Danecka and Edward Wallace
2025-07-18
Introduction
Candida glabrata strains:
- CBS138
- BG2
Treated with voriconazole (VCZ / VORI), fluconazole (FCZ / FLUC) or control with DMSO (solvent-only control, abbreviated CT).
Sequencing FASTQ files were aligned to appropriate genomes using HISAT2 and quantified using featureCounts.
MultiQC results, including quality control of raw reads (FastQC) and alignment are here:
- CBS138: ../data/multiQC/Candida_glabrata_CBS138/multiqc_report.html)
- BG2: ../data/multiQC/Candida_glabrata_BG2/multiqc_report.html)
featureCount results, aggregated by strain, are below:
counts_all_CBS138 = read.table("../data/featureCounts/Candida_glabrata_CBS138/CBS138_all_conditions_featureCounts.tab", header=TRUE)
counts_all_BG2 = read.table("../data/featureCounts/Candida_glabrata_BG2/BG2_all_conditions_featureCounts.tab", header=TRUE)
counts_rpm_CBS138 = read.table("../data/featureCounts/Candida_glabrata_CBS138/CBS138_all_conditions_rpm.tab", header=TRUE)
counts_rpm_BG2 = read.table("../data/featureCounts/Candida_glabrata_BG2/BG2_all_conditions_rpm.tab", header=TRUE)
head(counts_all_CBS138) # CBS138, raw## Geneid CBS138_RPMI_DMSO_A CBS138_RPMI_VORI_A CBS138_RPMI_FLUC_A
## 0 CAGL0A00165g 329 1277 953
## 1 CAGL0A00187g 541 1561 1755
## 2 CAGL0A00209g 2460 6237 7252
## 3 CAGL0A00231g 243 172 375
## 4 CAGL0A00253g 791 2009 2340
## 5 CAGL0A00275g 1295 2665 2876
## CBS138_RPMI_DMSO_B CBS138_RPMI_VORI_B CBS138_RPMI_FLUC_B CBS138_RPMI_DMSO_C
## 0 653 873 1124 422
## 1 1240 1434 1990 950
## 2 5037 6009 7581 3992
## 3 292 305 235 426
## 4 1336 2031 2071 1217
## 5 2133 2716 2933 1643
## CBS138_RPMI_VORI_C CBS138_RPMI_FLUC_C
## 0 436 3425
## 1 1120 7031
## 2 1345 18963
## 3 118 1572
## 4 395 8426
## 5 488 8892head(counts_all_BG2) # BG2, raw## Geneid BG2_RPMI_DMSO_A BG2_RPMI_VORI_A BG2_RPMI_FLUC_A BG2_RPMI_DMSO_B
## 0 GWK60_A00011 1 1 1 1
## 1 GWK60_A00033 100 169 93 116
## 2 GWK60_A00055 1490 2411 1982 1417
## 3 GWK60_A00077 4781 8038 6834 5852
## 4 GWK60_A00099 14463 20284 15228 15459
## 5 GWK60_A00121 2371 1412 816 2188
## BG2_RPMI_VORI_B BG2_RPMI_FLUC_B BG2_RPMI_DMSO_C BG2_RPMI_VORI_C
## 0 1 3 1 1
## 1 194 17 123 19
## 2 2422 304 1838 223
## 3 7534 1569 5704 1015
## 4 18965 2859 17357 1804
## 5 979 136 3000 63
## BG2_RPMI_FLUC_C
## 0 1
## 1 26
## 2 394
## 3 1236
## 4 2528
## 5 146Results normalised to RPM are below:
head(counts_rpm_CBS138) # CBS138, normalised to RPM## Geneid CBS138_RPMI_DMSO_A CBS138_RPMI_VORI_A CBS138_RPMI_FLUC_A
## 1 CAGL0A00165g 30.85212 65.75689 46.30258
## 2 CAGL0A00187g 50.73251 80.38097 85.26866
## 3 CAGL0A00209g 230.68756 321.16343 352.34663
## 4 CAGL0A00231g 22.78743 8.85684 18.21980
## 5 CAGL0A00253g 74.17637 103.44995 113.69155
## 6 CAGL0A00275g 121.43918 137.22953 139.73371
## CBS138_RPMI_DMSO_B CBS138_RPMI_VORI_B CBS138_RPMI_FLUC_B CBS138_RPMI_DMSO_C
## 1 38.03028 47.18167 51.79789 32.91856
## 2 72.21676 77.50116 91.70624 74.10577
## 3 293.35146 324.75904 349.35928 311.40026
## 4 17.00588 16.48386 10.82963 33.23059
## 5 77.80773 109.76629 95.43900 94.93340
## 6 124.22447 146.78741 135.16301 128.16398
## CBS138_RPMI_VORI_C CBS138_RPMI_FLUC_C
## 1 49.17631 46.07813
## 2 126.32448 94.59134
## 3 151.70216 255.11813
## 4 13.30919 21.14885
## 5 44.55194 113.35893
## 6 55.04138 119.62824head(counts_rpm_BG2) # BG2, normalised to RPM## Geneid BG2_RPMI_DMSO_A BG2_RPMI_VORI_A BG2_RPMI_FLUC_A BG2_RPMI_DMSO_B
## 1 GWK60_A00011 0.01411581 0.01238536 0.01580123 0.01571183
## 2 GWK60_A00033 1.41158064 2.09312569 1.46951436 1.82257193
## 3 GWK60_A00055 21.03255147 29.86110080 31.31803713 22.26365885
## 4 GWK60_A00077 67.48767020 99.55351647 107.98560331 91.94561156
## 5 GWK60_A00099 204.15690735 251.22462406 240.62112485 242.88913348
## 6 GWK60_A00121 33.46857687 17.48812705 12.89380338 34.37747746
## BG2_RPMI_VORI_B BG2_RPMI_FLUC_B BG2_RPMI_DMSO_C BG2_RPMI_VORI_C
## 1 0.0130404 0.2616564 0.01394962 0.1205643
## 2 2.5298376 1.4827197 1.71580380 2.2907212
## 3 31.5838485 26.5145175 25.63940963 26.8858332
## 4 98.2463727 136.8463092 79.56865753 122.3727387
## 5 247.3111836 249.3585711 242.12363055 217.4979513
## 6 12.7665515 11.8617578 41.84887317 7.5955493
## BG2_RPMI_FLUC_C
## 1 0.09884977
## 2 2.57009413
## 3 38.94681101
## 4 122.17832084
## 5 249.89222903
## 6 14.43206702Match genes across strains using Reciprocal Blast Best Hits
The genes between the two strains are matched using Reciprocal Blast Best Hits, which might not be entirely accurate given copy number variations etc. between the two species. I have used orthofinder https://doi.org/10.1186/s13059-019-1832-y to find orthologs, but I haven’t found a way to incorporate this into the analysis yet.
# Load reciprocal BLAST best hits
rbbh = read.csv("../data/rbbh/cbs138_bg2_rbbh2.csv")
# merge on CBS138 gene names,
counts_all_CBS138_rbbh = merge(counts_all_CBS138, rbbh,
by.x="Geneid", by.y="gene_id_cbs138")
# combine counts from common genes.
counts_all_joined = merge(counts_all_CBS138_rbbh,
dplyr::rename(counts_all_BG2, gene_id_bg2 = "Geneid"),
by = "gene_id_bg2")
head(counts_all_joined)## gene_id_bg2 Geneid CBS138_RPMI_DMSO_A CBS138_RPMI_VORI_A
## 1 GWK60_A00011 CAGL0H10626g 119 153
## 2 GWK60_A00055 CAGL0A00165g 329 1277
## 3 GWK60_A00077 CAGL0A00187g 541 1561
## 4 GWK60_A00099 CAGL0A00209g 2460 6237
## 5 GWK60_A00121 CAGL0A00231g 243 172
## 6 GWK60_A00143 CAGL0A00253g 791 2009
## CBS138_RPMI_FLUC_A CBS138_RPMI_DMSO_B CBS138_RPMI_VORI_B CBS138_RPMI_FLUC_B
## 1 371 218 354 317
## 2 953 653 873 1124
## 3 1755 1240 1434 1990
## 4 7252 5037 6009 7581
## 5 375 292 305 235
## 6 2340 1336 2031 2071
## CBS138_RPMI_DMSO_C CBS138_RPMI_VORI_C CBS138_RPMI_FLUC_C BG2_RPMI_DMSO_A
## 1 238 205 2307 1
## 2 422 436 3425 1490
## 3 950 1120 7031 4781
## 4 3992 1345 18963 14463
## 5 426 118 1572 2371
## 6 1217 395 8426 5403
## BG2_RPMI_VORI_A BG2_RPMI_FLUC_A BG2_RPMI_DMSO_B BG2_RPMI_VORI_B
## 1 1 1 1 1
## 2 2411 1982 1417 2422
## 3 8038 6834 5852 7534
## 4 20284 15228 15459 18965
## 5 1412 816 2188 979
## 6 8274 5540 4938 6905
## BG2_RPMI_FLUC_B BG2_RPMI_DMSO_C BG2_RPMI_VORI_C BG2_RPMI_FLUC_C
## 1 3 1 1 1
## 2 304 1838 223 394
## 3 1569 5704 1015 1236
## 4 2859 17357 1804 2528
## 5 136 3000 63 146
## 6 984 5687 608 1004Analysis
Quality control - sample correlation
For quality control, we check correlation between the samples (only within strain).
There is high correlation within control (DMSO) samples and treated (FCZ and VCZ), but no obvious differences between VCZ and FCZ.
This shows that the replicates are generally very well correlated, R > 0.96. However, there is more variability in replicate C, especially CBS138_RPMI_VORI_C.
Quality control - clustering
We intially cluster the results on raw rpm, separately by strain. Again untreated samples cluster together and treated samples cluster together. Treated samples cluster in a way that doesn’t indicate any obvious sample mix-up.
CBS138_RPMI_VORI_C is an outlier.
Calculate rlog
Regularized logarithm, on both strains together joined by best-hit genes.
sample_sheet_all = here::here("data",
"sample_sheets",
"DGE_samplesheet_canGla2.txt") %>%
read_table()##
## ── Column specification ────────────────────────────────────────────────────────
## cols(
## SampleID = col_double(),
## Code = col_character(),
## Medium = col_character(),
## Temp = col_character(),
## Time = col_character(),
## Rep = col_character(),
## Species = col_character(),
## Strain = col_character(),
## Condition = col_character()
## )# samplesheet = py$experiment_data_both
rownames(sample_sheet_all) = sample_sheet_all$Code## Warning: Setting row names on a tibble is deprecated.print(sample_sheet_all)## # A tibble: 18 × 9
## SampleID Code Medium Temp Time Rep Species Strain Condition
## * <dbl> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr>
## 1 86 CBS138_RPMI_DMSO_A RPMI_… 37C 4h A Candid… CBS138 CBS138_R…
## 2 87 CBS138_RPMI_VORI_A RPMI_… 37C 4h A Candid… CBS138 CBS138_R…
## 3 88 CBS138_RPMI_FLUC_A RPMI_… 37C 4h A Candid… CBS138 CBS138_R…
## 4 89 BG2_RPMI_DMSO_A RPMI_… 37C 4h A Candid… BG2 BG2_RPMI…
## 5 90 BG2_RPMI_VORI_A RPMI_… 37C 4h A Candid… BG2 BG2_RPMI…
## 6 91 BG2_RPMI_FLUC_A RPMI_… 37C 4h A Candid… BG2 BG2_RPMI…
## 7 92 CBS138_RPMI_DMSO_B RPMI_… 37C 4h B Candid… CBS138 CBS138_R…
## 8 93 CBS138_RPMI_VORI_B RPMI_… 37C 4h B Candid… CBS138 CBS138_R…
## 9 94 CBS138_RPMI_FLUC_B RPMI_… 37C 4h B Candid… CBS138 CBS138_R…
## 10 98 BG2_RPMI_DMSO_B RPMI_… 37C 4h B Candid… BG2 BG2_RPMI…
## 11 99 BG2_RPMI_VORI_B RPMI_… 37C 4h B Candid… BG2 BG2_RPMI…
## 12 100 BG2_RPMI_FLUC_B RPMI_… 37C 4h B Candid… BG2 BG2_RPMI…
## 13 95 CBS138_RPMI_DMSO_C RPMI_… 37C 4h C Candid… CBS138 CBS138_R…
## 14 96 CBS138_RPMI_VORI_C RPMI_… 37C 4h C Candid… CBS138 CBS138_R…
## 15 97 CBS138_RPMI_FLUC_C RPMI_… 37C 4h C Candid… CBS138 CBS138_R…
## 16 101 BG2_RPMI_DMSO_C RPMI_… 37C 4h C Candid… BG2 BG2_RPMI…
## 17 102 BG2_RPMI_VORI_C RPMI_… 37C 4h C Candid… BG2 BG2_RPMI…
## 18 103 BG2_RPMI_FLUC_C RPMI_… 37C 4h C Candid… BG2 BG2_RPMI…dds_all <- DESeqDataSetFromMatrix(countData =
counts_all_joined %>%
dplyr::select(sample_sheet_all$Code) %>%
magrittr::set_rownames(counts_all_joined$Gene),
colData = sample_sheet_all,
design = ~ Code)## Warning in DESeqDataSet(se, design = design, ignoreRank): some variables in
## design formula are characters, converting to factorsrlog_all <- rlog(dds_all)
head(assay(rlog_all))## CBS138_RPMI_DMSO_A CBS138_RPMI_VORI_A CBS138_RPMI_FLUC_A
## CAGL0H10626g 7.532662 7.046592 7.803483
## CAGL0A00165g 9.819161 10.247470 9.981287
## CAGL0A00187g 10.850525 11.007853 11.079555
## CAGL0A00209g 12.708113 12.783775 12.891339
## CAGL0A00231g 9.134426 8.283834 8.798710
## CAGL0A00253g 11.102017 11.177522 11.284519
## BG2_RPMI_DMSO_A BG2_RPMI_VORI_A BG2_RPMI_FLUC_A CBS138_RPMI_DMSO_B
## CAGL0H10626g 5.262604 5.237443 5.253129 7.578427
## CAGL0A00165g 9.575449 9.699059 9.706994 9.911436
## CAGL0A00187g 11.105937 11.269220 11.305368 11.037381
## CAGL0A00209g 12.660509 12.678386 12.613487 12.830194
## CAGL0A00231g 9.522984 8.829991 8.578657 8.830633
## CAGL0A00253g 11.176013 11.266810 11.107186 11.065763
## CBS138_RPMI_VORI_B CBS138_RPMI_FLUC_B BG2_RPMI_DMSO_B
## CAGL0H10626g 7.866795 7.604660 5.264334
## CAGL0A00165g 10.004430 10.069135 9.552677
## CAGL0A00187g 11.013891 11.131689 11.283900
## CAGL0A00209g 12.830300 12.878901 12.730468
## CAGL0A00231g 8.731257 8.427881 9.468714
## CAGL0A00253g 11.263050 11.135540 11.118469
## BG2_RPMI_VORI_B BG2_RPMI_FLUC_B CBS138_RPMI_DMSO_C
## CAGL0H10626g 5.239410 5.617187 7.879963
## CAGL0A00165g 9.723904 9.631222 9.758397
## CAGL0A00187g 11.239058 11.554708 11.019457
## CAGL0A00209g 12.646469 12.694132 12.838603
## CAGL0A00231g 8.581103 8.570093 9.332638
## CAGL0A00253g 11.140956 11.142942 11.186040
## CBS138_RPMI_VORI_C CBS138_RPMI_FLUC_C BG2_RPMI_DMSO_C
## CAGL0H10626g 8.178808 8.388479 5.254219
## CAGL0A00165g 10.166875 10.021087 9.659647
## CAGL0A00187g 11.533233 11.203325 11.169054
## CAGL0A00209g 12.350243 12.666644 12.730393
## CAGL0A00231g 8.690081 8.954762 9.647514
## CAGL0A00253g 10.688575 11.326460 11.138934
## BG2_RPMI_VORI_C BG2_RPMI_FLUC_C
## CAGL0H10626g 5.606251 5.549291
## CAGL0A00165g 9.623289 9.889308
## CAGL0A00187g 11.440342 11.419485
## CAGL0A00209g 12.563927 12.655815
## CAGL0A00231g 8.276823 8.672952
## CAGL0A00253g 10.997610 11.221235rlog_all_df = as.data.frame(assay(rlog_all))Clustering on rlog across strains
Clustering on normalized rlog across strains
Normalized rlog gets at relative (not absolute) differences in expression between strains. Here we additionally filter for a minimal count of 100, to remove low-count noise.
These clustering analyses support:
- clustering by - / + drug dominates clustering by strain
- the difference between the two drugs is minimal
- within drug treated samples, strains cluster.
- CBS138_RPMI_VORI_C is an outlier
We are not trying to get any more information out of this analysis, e.g. not trying to identify clusters of co-regulated genes, so there is no need to do more arranging the plots.
Quality Control - Principal Component Analysis
Calculate principal components from rlog.
# calculate principal components of rlog, after extracting from the dataset
pca_rlog <- rlog_all %>%
assay() %>%
t() %>%
prcomp()
# convert principal components to data frame
pcdf_rlog <- bind_cols(
as_tibble(colData(rlog_all)),
as_tibble(pca_rlog$x)
)
pcdf_rlog## # A tibble: 18 × 28
## SampleID Code Medium Temp Time Rep Species Strain Condition sizeFactor
## <dbl> <fct> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <dbl>
## 1 86 CBS138… RPMI_… 37C 4h A Candid… CBS138 CBS138_R… 0.368
## 2 87 CBS138… RPMI_… 37C 4h A Candid… CBS138 CBS138_R… 0.851
## 3 88 CBS138… RPMI_… 37C 4h A Candid… CBS138 CBS138_R… 0.870
## 4 89 BG2_RP… RPMI_… 37C 4h A Candid… BG2 BG2_RPMI… 2.29
## 5 90 BG2_RP… RPMI_… 37C 4h A Candid… BG2 BG2_RPMI… 3.14
## 6 91 BG2_RP… RPMI_… 37C 4h A Candid… BG2 BG2_RPMI… 2.56
## 7 92 CBS138… RPMI_… 37C 4h B Candid… CBS138 CBS138_R… 0.650
## 8 93 CBS138… RPMI_… 37C 4h B Candid… CBS138 CBS138_R… 0.775
## 9 94 CBS138… RPMI_… 37C 4h B Candid… CBS138 CBS138_R… 0.923
## 10 98 BG2_RP… RPMI_… 37C 4h B Candid… BG2 BG2_RPMI… 2.25
## 11 99 BG2_RP… RPMI_… 37C 4h B Candid… BG2 BG2_RPMI… 3.06
## 12 100 BG2_RP… RPMI_… 37C 4h B Candid… BG2 BG2_RPMI… 0.435
## 13 95 CBS138… RPMI_… 37C 4h C Candid… CBS138 CBS138_R… 0.510
## 14 96 CBS138… RPMI_… 37C 4h C Candid… CBS138 CBS138_R… 0.318
## 15 97 CBS138… RPMI_… 37C 4h C Candid… CBS138 CBS138_R… 2.98
## 16 101 BG2_RP… RPMI_… 37C 4h C Candid… BG2 BG2_RPMI… 2.52
## 17 102 BG2_RP… RPMI_… 37C 4h C Candid… BG2 BG2_RPMI… 0.323
## 18 103 BG2_RP… RPMI_… 37C 4h C Candid… BG2 BG2_RPMI… 0.403
## # ℹ 18 more variables: PC1 <dbl>, PC2 <dbl>, PC3 <dbl>, PC4 <dbl>, PC5 <dbl>,
## # PC6 <dbl>, PC7 <dbl>, PC8 <dbl>, PC9 <dbl>, PC10 <dbl>, PC11 <dbl>,
## # PC12 <dbl>, PC13 <dbl>, PC14 <dbl>, PC15 <dbl>, PC16 <dbl>, PC17 <dbl>,
## # PC18 <dbl>propvar_rlog_df <- tibble(
PC = seq.int(1L, ncol(pca_rlog$x) ),
tot_var = pca_rlog$sdev^2,
prop_var = tot_var/sum(tot_var)
)
propvar_rlog_df## # A tibble: 18 × 3
## PC tot_var prop_var
## <int> <dbl> <dbl>
## 1 1 1.68e+ 2 3.58e- 1
## 2 2 1.55e+ 2 3.31e- 1
## 3 3 6.87e+ 1 1.46e- 1
## 4 4 1.82e+ 1 3.88e- 2
## 5 5 1.60e+ 1 3.40e- 2
## 6 6 1.26e+ 1 2.68e- 2
## 7 7 5.75e+ 0 1.22e- 2
## 8 8 4.79e+ 0 1.02e- 2
## 9 9 3.80e+ 0 8.08e- 3
## 10 10 3.32e+ 0 7.07e- 3
## 11 11 3.07e+ 0 6.54e- 3
## 12 12 2.48e+ 0 5.28e- 3
## 13 13 2.09e+ 0 4.45e- 3
## 14 14 1.78e+ 0 3.79e- 3
## 15 15 1.29e+ 0 2.75e- 3
## 16 16 1.14e+ 0 2.44e- 3
## 17 17 1.04e+ 0 2.21e- 3
## 18 18 1.07e-26 2.29e-29plot_percentvar_rlog <-
ggplot(data = propvar_rlog_df,
aes(x = PC, y = prop_var)) +
geom_col(fill = "skyblue3") +
scale_x_continuous("principal component",
limits = c(0.4,10.6),
breaks = 1L:10L,
expand = c(0,0)) +
scale_y_continuous("prop. of variance", expand = c(0,0))
plot_percentvar_rlog## Warning: Removed 8 rows containing missing values or values outside the scale range
## (`geom_col()`).
scales_PCA <-
list(
scale_colour_manual("Strain, Treatment",
values = c("CBS138_RPMI_DMSO" = "grey20",
"CBS138_RPMI_FLUC" = "purple3",
"CBS138_RPMI_VORI" = "green4",
"BG2_RPMI_DMSO" = "grey20",
"BG2_RPMI_FLUC" = "purple3",
"BG2_RPMI_VORI" = "green4"),
labels = c("CBS138_RPMI_DMSO" = "CBS138, CT",
"CBS138_RPMI_FLUC" = "CBS138, FCZ",
"CBS138_RPMI_VORI" = "CBS138, VCZ",
"BG2_RPMI_DMSO" = "BG2, CT",
"BG2_RPMI_FLUC" = "BG2, FCZ",
"BG2_RPMI_VORI" = "BG2, VCZ")),
scale_shape_manual("Strain, Treatment",
values = c("CBS138_RPMI_DMSO" = 16,
"CBS138_RPMI_FLUC" = 16,
"CBS138_RPMI_VORI" = 16,
"BG2_RPMI_DMSO" = 17,
"BG2_RPMI_FLUC" = 17,
"BG2_RPMI_VORI" = 17),
labels = c("CBS138_RPMI_DMSO" = "CBS138, CT",
"CBS138_RPMI_FLUC" = "CBS138, FCZ",
"CBS138_RPMI_VORI" = "CBS138, VCZ",
"BG2_RPMI_DMSO" = "BG2, CT",
"BG2_RPMI_FLUC" = "BG2, FCZ",
"BG2_RPMI_VORI" = "BG2, VCZ"))
)
pc12 = ggplot(data = pcdf_rlog,
aes(colour = Condition, shape = Condition)
) +
geom_hline(yintercept = 0, colour = "grey90") +
geom_vline(xintercept = 0, colour = "grey90") +
geom_point(aes(x = PC1, y = PC2), size = 2) +
theme(legend.box = "horizontal") +
scales_PCA
legend = get_legend(pc12)## Warning in grid.Call(C_stringMetric, as.graphicsAnnot(x$label)): font family
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## returning the first one. To return all, use `return_all = TRUE`.pc12
pc32 = ggplot(data = pcdf_rlog,
aes(colour = Condition, shape = Condition)
) +
geom_hline(yintercept = 0, colour = "grey90") +
geom_vline(xintercept = 0, colour = "grey90") +
geom_point(aes(x = PC3, y = PC2), size = 2) +
scales_PCA
pc32
ggplot(data = pcdf_rlog,
aes(colour = Condition, shape = Rep)
) +
geom_point(aes(x = PC3, y = PC2)) +
scale_shape_identity()
# TODO: change styling to include shapes: circles squares triangles, maybe add Vs and FsConclusions:
In PC1 vs PC2 there are 4 clear clusters: corresponding to treated and untreated strains BG2 and CBS138. In PC3 they look more similar.
The outlier: CBS138_RPMI_VORI_C (light purple) clusters with other bio reps in PC1-PC2, but not in PC3. After discussion, we decided that something was not quite right in that replicate.
Differential Gene Expression analysis using DESeq2 in each strain separately
Differential Gene Expression analysis was performed using DESeq2. Genes with adjusted p-value < 0.05 and at least 2x change are considered differentially expressed here. The upregulated and downregulated genes are saved in ../data/deseq2
DGE, CBS138, FCZ vs CT
dds_compared_conditions_cf =
run_deseq_vsmedium(counts_all_CBS138,
conditions_to_compare = c("CBS138_RPMI_DMSO", "CBS138_RPMI_FLUC"),
strains_to_include = "CBS138")
dds_compared_conditions_cf## class: DESeqDataSet
## dim: 5209 6
## metadata(1): version
## assays(4): counts mu H cooks
## rownames(5209): CAGL0A00165g CAGL0A00187g ... CaglfMp11 CaglfMp12
## rowData names(22): baseMean baseVar ... deviance maxCooks
## colnames(6): CBS138_RPMI_DMSO_A CBS138_RPMI_FLUC_A ...
## CBS138_RPMI_DMSO_C CBS138_RPMI_FLUC_C
## colData names(10): SampleID Code ... Condition sizeFactorresults(dds_compared_conditions_cf)## log2 fold change (MLE): Medium RPMI FLUC vs RPMI DMSO
## Wald test p-value: Medium RPMI FLUC vs RPMI DMSO
## DataFrame with 5209 rows and 6 columns
## baseMean log2FoldChange lfcSE stat pvalue padj
## <numeric> <numeric> <numeric> <numeric> <numeric> <numeric>
## CAGL0A00165g 836.639 0.3197520 0.174032 1.8373124 0.0661638 0.1263219
## CAGL0A00187g 1591.597 0.2931970 0.179392 1.6343944 0.1021761 0.1790316
## CAGL0A00209g 6112.252 0.0175113 0.178075 0.0983363 0.9216652 0.9458500
## CAGL0A00231g 428.139 -0.6982981 0.308496 -2.2635540 0.0236016 0.0542966
## CAGL0A00253g 1940.918 0.2130427 0.173391 1.2286835 0.2191905 0.3298048
## ... ... ... ... ... ... ...
## CaglfMp08 1.19313 -1.383433 2.018901 -0.6852404 0.4931923 NA
## CaglfMp09 14.09621 0.318143 0.768816 0.4138090 0.6790140 NA
## CaglfMp10 1.55326 -0.160372 1.784641 -0.0898622 0.9283967 NA
## CaglfMp11 515.40070 -0.557760 0.296941 -1.8783528 0.0603329 0.117155
## CaglfMp12 9.10294 0.419579 1.024048 0.4097258 0.6820071 NArN = resultsNames(dds_compared_conditions_cf)
rN## [1] "Intercept" "Medium_RPMI_FLUC_vs_RPMI_DMSO"deseq_df_cf <- deseq_df_transform(dds_compared_conditions_cf,
termstokeep = rN[2])
DEGdf_up2x_FDR5_cf = get_upregulated_genes(deseq_df_cf)
DEGdf_down2x_FDR5_cf = get_downregulated_genes(deseq_df_cf)
DEGdf_non_significant_cf = get_non_significant_genes(deseq_df_cf)
write.csv(deseq_df_cf, "../data/DESeq2/CBS138/CBS138_FLUC_DMSO_allDESeq.csv")
p_cf = volcano_plot(deseq_df_cf, DEGdf_up2x_FDR5_cf, DEGdf_down2x_FDR5_cf,
xlabel = "log2 fold-change\n← down, FCZ up, FCZ →") +
ggtitle("FCZ vs CT, Strain CBS138")
#p_cfDGE, CBS138, VCZ vs CT
dds_compared_conditions_cv =
run_deseq_vsmedium(counts_all_CBS138,
conditions_to_compare = c("CBS138_RPMI_DMSO", "CBS138_RPMI_VORI"),
strains_to_include = "CBS138")
dds_compared_conditions_cv## class: DESeqDataSet
## dim: 5209 6
## metadata(1): version
## assays(4): counts mu H cooks
## rownames(5209): CAGL0A00165g CAGL0A00187g ... CaglfMp11 CaglfMp12
## rowData names(22): baseMean baseVar ... deviance maxCooks
## colnames(6): CBS138_RPMI_DMSO_A CBS138_RPMI_VORI_A ...
## CBS138_RPMI_DMSO_C CBS138_RPMI_VORI_C
## colData names(10): SampleID Code ... Condition sizeFactorresults(dds_compared_conditions_cv)## log2 fold change (MLE): Medium RPMI VORI vs RPMI DMSO
## Wald test p-value: Medium RPMI VORI vs RPMI DMSO
## DataFrame with 5209 rows and 6 columns
## baseMean log2FoldChange lfcSE stat pvalue padj
## <numeric> <numeric> <numeric> <numeric> <numeric> <numeric>
## CAGL0A00165g 602.177 0.5489343 0.253149 2.168422 0.0301266 0.107496
## CAGL0A00187g 1114.970 0.4538980 0.354983 1.278649 0.2010207 0.391611
## CAGL0A00209g 3724.394 -0.2077371 0.312624 -0.664496 0.5063732 0.691691
## CAGL0A00231g 260.923 -1.0150217 0.406456 -2.497247 0.0125162 0.057835
## CAGL0A00253g 1147.867 -0.0838943 0.345653 -0.242713 0.8082281 0.898777
## ... ... ... ... ... ... ...
## CaglfMp08 1.05901 -0.228622 2.10445 -0.108637 0.91349024 NA
## CaglfMp09 7.31921 -0.385422 1.07051 -0.360036 0.71881991 0.8484567
## CaglfMp10 1.05901 -0.228622 2.10445 -0.108637 0.91349024 NA
## CaglfMp11 281.70578 -1.337513 0.51890 -2.577593 0.00994911 0.0494646
## CaglfMp12 4.71152 -0.162560 1.34394 -0.120958 0.90372448 0.9500550rN = resultsNames(dds_compared_conditions_cv)
rN## [1] "Intercept" "Medium_RPMI_VORI_vs_RPMI_DMSO"deseq_df_cv <- deseq_df_transform(dds_compared_conditions_cv,
termstokeep = rN[2])
DEGdf_up2x_FDR5_cv = get_upregulated_genes(deseq_df_cv)
DEGdf_down2x_FDR5_cv = get_downregulated_genes(deseq_df_cv)
DEGdf_non_significant_cv = get_non_significant_genes(deseq_df_cv)
write.csv(deseq_df_cv, "../data/DESeq2/CBS138/CBS138_VORI_DMSO_allDESeq.csv")
p_cv = volcano_plot(deseq_df_cv, DEGdf_up2x_FDR5_cv, DEGdf_down2x_FDR5_cv,
xlabel = "log2 fold-change\n← down, VCZ up, VCZ →") +
ggtitle("VCZ vs CT, Strain CBS138")
#p_cvCheck: DGE, CBS138, FCZ vs CT excluding the outlying sample CBS138_RPMI_VORI_C
Conclude: the single outlying sample CBS138_RPMI_VORI_C
has minimal effect on the substantial results. Although it changes the
genelists over the cutoff, it doesn’t change much most of the fold
changes and p-values.
dds_compared_conditions_xc =
run_deseq_vsmedium(counts_all_CBS138,
conditions_to_compare = c("CBS138_RPMI_DMSO", "CBS138_RPMI_VORI"),
strains_to_include = "CBS138",
sample_sheet = dplyr::filter(sample_sheet_all,
Code != "CBS138_RPMI_VORI_C"))
dds_compared_conditions_xc## class: DESeqDataSet
## dim: 5209 5
## metadata(1): version
## assays(4): counts mu H cooks
## rownames(5209): CAGL0A00165g CAGL0A00187g ... CaglfMp11 CaglfMp12
## rowData names(22): baseMean baseVar ... deviance maxCooks
## colnames(5): CBS138_RPMI_DMSO_A CBS138_RPMI_VORI_A CBS138_RPMI_DMSO_B
## CBS138_RPMI_VORI_B CBS138_RPMI_DMSO_C
## colData names(10): SampleID Code ... Condition sizeFactorresults(dds_compared_conditions_xc)## log2 fold change (MLE): Medium RPMI VORI vs RPMI DMSO
## Wald test p-value: Medium RPMI VORI vs RPMI DMSO
## DataFrame with 5209 rows and 6 columns
## baseMean log2FoldChange lfcSE stat pvalue
## <numeric> <numeric> <numeric> <numeric> <numeric>
## CAGL0A00165g 644.278 0.5271746 0.250260 2.1065089 0.03516017
## CAGL0A00187g 1074.564 0.0717238 0.227601 0.3151291 0.75266364
## CAGL0A00209g 4496.242 0.0194891 0.197717 0.0985705 0.92147929
## CAGL0A00231g 306.054 -1.1249116 0.399868 -2.8132084 0.00490498
## CAGL0A00253g 1393.269 0.1775422 0.206492 0.8598024 0.38989797
## ... ... ... ... ... ...
## CaglfMp08 1.04557 -0.72864009 2.344279 -0.31081633 0.7559403
## CaglfMp09 9.46857 0.00909591 0.944194 0.00963351 0.9923137
## CaglfMp10 1.04557 -0.72864009 2.344279 -0.31081633 0.7559403
## CaglfMp11 348.06393 -1.23921807 0.516927 -2.39727857 0.0165174
## CaglfMp12 5.94529 0.16932639 1.274728 0.13283340 0.8943251
## padj
## <numeric>
## CAGL0A00165g 0.0963664
## CAGL0A00187g 0.8409401
## CAGL0A00209g 0.9499427
## CAGL0A00231g 0.0209321
## CAGL0A00253g 0.5471509
## ... ...
## CaglfMp08 NA
## CaglfMp09 NA
## CaglfMp10 NA
## CaglfMp11 0.0529289
## CaglfMp12 NArN = resultsNames(dds_compared_conditions_xc)
rN## [1] "Intercept" "Medium_RPMI_VORI_vs_RPMI_DMSO"deseq_df_xc <- deseq_df_transform(dds_compared_conditions_xc,
termstokeep = rN[2])
DEGdf_up2x_FDR5_cvxc = get_upregulated_genes(deseq_df_xc)
DEGdf_down2x_FDR5_cvxc = get_downregulated_genes(deseq_df_xc)
DEGdf_non_significant_cvxc = get_non_significant_genes(deseq_df_xc)
# write.csv(deseq_df_xc, "../data/DESeq2/CBS138/CBS138_VORI_DMSO_allDESeq.csv")
p_cvx = volcano_plot(deseq_df_xc, DEGdf_up2x_FDR5_cvxc, DEGdf_down2x_FDR5_cvxc,
xlabel = "log2 fold-change\n← down, VCZ up, VCZ →") +
ggtitle("VCZ vs CT, Strain CBS138, exclude outlying sample")
#p_cvx
deseq_df_3repsvsxc <-
dplyr::inner_join(deseq_df_cv,
deseq_df_xc,
by = "gene",
suffix = c(".all", ".xc"))
ggplot(data = deseq_df_3repsvsxc, aes(x = log2FC.all, y = log2FC.xc)) +
geom_hline(yintercept = c(-1, 1), colour = "purple", linetype = "dashed") +
geom_vline(xintercept = c(-1, 1), colour = "purple", linetype = "dashed") +
geom_abline(intercept = 0, slope = 1, colour = "purple") +
geom_point(size = 0.2, colour = "grey50") +
geom_point(data = dplyr::filter(deseq_df_3repsvsxc,
gene %in% DEGdf_up2x_FDR5_cvxc$gene),
size = 1, colour = "darkblue") +
geom_point(data = dplyr::filter(deseq_df_3repsvsxc,
gene %in% DEGdf_down2x_FDR5_cvxc$gene),
size = 1, colour = "darkred")
DGE, CBS138, VCZ vs FCZ
dds_compared_conditions_cvf <-
run_deseq_vsmedium(counts_all_CBS138,
conditions_to_compare = c("CBS138_RPMI_FLUC", "CBS138_RPMI_VORI"),
strains_to_include = "CBS138")
dds_compared_conditions_cvf## class: DESeqDataSet
## dim: 5209 6
## metadata(1): version
## assays(4): counts mu H cooks
## rownames(5209): CAGL0A00165g CAGL0A00187g ... CaglfMp11 CaglfMp12
## rowData names(22): baseMean baseVar ... deviance maxCooks
## colnames(6): CBS138_RPMI_VORI_A CBS138_RPMI_FLUC_A ...
## CBS138_RPMI_VORI_C CBS138_RPMI_FLUC_C
## colData names(10): SampleID Code ... Condition sizeFactorresults(dds_compared_conditions_cvf)## log2 fold change (MLE): Medium RPMI VORI vs RPMI FLUC
## Wald test p-value: Medium RPMI VORI vs RPMI FLUC
## DataFrame with 5209 rows and 6 columns
## baseMean log2FoldChange lfcSE stat pvalue padj
## <numeric> <numeric> <numeric> <numeric> <numeric> <numeric>
## CAGL0A00165g 1101.737 0.207888 0.209804 0.990867 0.321751 0.735696
## CAGL0A00187g 2030.501 0.142320 0.337058 0.422242 0.672849 0.871859
## CAGL0A00209g 6232.873 -0.246693 0.309467 -0.797152 0.425363 0.783094
## CAGL0A00231g 322.077 -0.332331 0.420327 -0.790648 0.429149 0.786189
## CAGL0A00253g 2064.212 -0.317729 0.337930 -0.940222 0.347104 0.745921
## ... ... ... ... ... ... ...
## CaglfMp08 1.20986 1.128652 2.015912 0.5598716 0.5755670 0.836253
## CaglfMp09 13.45210 -0.687300 0.978899 -0.7021156 0.4826071 0.804700
## CaglfMp10 1.60583 -0.102210 1.799630 -0.0567951 0.9547084 0.982067
## CaglfMp11 360.79854 -0.796753 0.473493 -1.6827120 0.0924309 0.664200
## CaglfMp12 9.45453 -0.620352 1.265478 -0.4902118 0.6239840 0.852734rN = resultsNames(dds_compared_conditions_cvf)
rN## [1] "Intercept" "Medium_RPMI_VORI_vs_RPMI_FLUC"deseq_df_cvf <- deseq_df_transform(dds_compared_conditions_cvf,
termstokeep = rN[2])
DEGdf_up2x_FDR5_cvf = get_upregulated_genes(deseq_df_cvf)
DEGdf_down2x_FDR5_cvf = get_downregulated_genes(deseq_df_cvf)
DEGdf_non_significant_cvf = get_non_significant_genes(deseq_df_cvf)
write.csv(deseq_df_cvf, "../data/DESeq2/CBS138/CBS138_VORI_FLUC_allDESeq.csv")
p_cvf = volcano_plot(deseq_df_cvf, DEGdf_up2x_FDR5_cvf, DEGdf_down2x_FDR5_cvf,
xlabel = "log2 fold-change\n← up, FCZ up, VCZ →") +
ggtitle("VCZ vs FCZ, Strain CBS138")
#p_cvfDouble-check: DGE, CBS138, VCZ vs FCZ excluding the outlying sample CBS138_RPMI_VORI_C
dds_compared_conditions_cvfxc <-
run_deseq_vsmedium(counts_all_CBS138,
conditions_to_compare = c("CBS138_RPMI_FLUC", "CBS138_RPMI_VORI"),
strains_to_include = "CBS138",
sample_sheet = dplyr::filter(sample_sheet_all,
Code != "CBS138_RPMI_VORI_C"))
dds_compared_conditions_cvfxc## class: DESeqDataSet
## dim: 5209 5
## metadata(1): version
## assays(4): counts mu H cooks
## rownames(5209): CAGL0A00165g CAGL0A00187g ... CaglfMp11 CaglfMp12
## rowData names(22): baseMean baseVar ... deviance maxCooks
## colnames(5): CBS138_RPMI_VORI_A CBS138_RPMI_FLUC_A CBS138_RPMI_VORI_B
## CBS138_RPMI_FLUC_B CBS138_RPMI_FLUC_C
## colData names(10): SampleID Code ... Condition sizeFactorresults(dds_compared_conditions_cvfxc)## log2 fold change (MLE): Medium RPMI VORI vs RPMI FLUC
## Wald test p-value: Medium RPMI VORI vs RPMI FLUC
## DataFrame with 5209 rows and 6 columns
## baseMean log2FoldChange lfcSE stat pvalue padj
## <numeric> <numeric> <numeric> <numeric> <numeric> <numeric>
## CAGL0A00165g 1326.551 0.1862951 0.202049 0.9220281 0.356514 0.804471
## CAGL0A00187g 2225.827 -0.2420684 0.164808 -1.4687912 0.141889 0.717400
## CAGL0A00209g 8281.619 -0.0190084 0.194410 -0.0977745 0.922111 0.985455
## CAGL0A00231g 394.159 -0.4441326 0.393893 -1.1275448 0.259512 0.777751
## CAGL0A00253g 2776.539 -0.0556065 0.186938 -0.2974592 0.766116 0.955101
## ... ... ... ... ... ... ...
## CaglfMp08 1.09792 0.613396 2.467883 0.248552 0.803708 0.962591
## CaglfMp09 19.15890 -0.318339 0.867010 -0.367169 0.713493 0.937821
## CaglfMp10 1.67950 -0.571602 2.132226 -0.268078 0.788639 0.962591
## CaglfMp11 477.06310 -0.699553 0.441275 -1.585301 0.112898 0.715920
## CaglfMp12 13.27455 -0.279166 1.192923 -0.234018 0.814971 0.965527rN = resultsNames(dds_compared_conditions_cvfxc)
rN## [1] "Intercept" "Medium_RPMI_VORI_vs_RPMI_FLUC"deseq_df_cvfxc <- deseq_df_transform(dds_compared_conditions_cvfxc,
termstokeep = rN[2])
DEGdf_up2x_FDR5_cvfxc = get_upregulated_genes(deseq_df_cvfxc)
DEGdf_down2x_FDR5_cvfxc = get_downregulated_genes(deseq_df_cvfxc)
volcano_plot(deseq_df_cvfxc, DEGdf_up2x_FDR5_cvfxc, DEGdf_down2x_FDR5_cvfxc,
xlabel = "log2 fold-change\n← up, FCZ up, VCZ →") +
ggtitle("VCZ vs FCZ, Strain CBS138")
Again this does not substantially change outcome: 7 DE genes when the sample is excluded, instead of zero.
DGE, BG2, FCZ vs CT
dds_compared_conditions_bf =
run_deseq_vsmedium(counts_all_BG2,
conditions_to_compare = c("BG2_RPMI_DMSO", "BG2_RPMI_FLUC"),
strains_to_include = "BG2")
dds_compared_conditions_bf## class: DESeqDataSet
## dim: 5234 6
## metadata(1): version
## assays(4): counts mu H cooks
## rownames(5234): GWK60_A00011 GWK60_A00033 ... GWK60_M14047 GWK60_M14597
## rowData names(22): baseMean baseVar ... deviance maxCooks
## colnames(6): BG2_RPMI_DMSO_A BG2_RPMI_FLUC_A ... BG2_RPMI_DMSO_C
## BG2_RPMI_FLUC_C
## colData names(10): SampleID Code ... Condition sizeFactorresults(dds_compared_conditions_bf)## log2 fold change (MLE): Medium RPMI FLUC vs RPMI DMSO
## Wald test p-value: Medium RPMI FLUC vs RPMI DMSO
## DataFrame with 5234 rows and 6 columns
## baseMean log2FoldChange lfcSE stat pvalue padj
## <numeric> <numeric> <numeric> <numeric> <numeric> <numeric>
## GWK60_A00011 2.45412 2.770152 1.811888 1.528876 0.12629510 0.190938
## GWK60_A00033 63.40106 -0.112474 0.369791 -0.304155 0.76100947 0.820924
## GWK60_A00055 994.93649 0.262738 0.158995 1.652484 0.09843592 0.154071
## GWK60_A00077 3634.13071 0.404350 0.148619 2.720713 0.00651413 0.013871
## GWK60_A00099 8677.47644 -0.115410 0.102964 -1.120876 0.26234046 0.354232
## ... ... ... ... ... ... ...
## GWK60_M13981 295.28461 -0.387677 0.229315 -1.690587 0.09091563 0.1444603
## GWK60_M14003 165.85087 0.337904 0.265481 1.272800 0.20308897 0.2852308
## GWK60_M14025 657.87791 0.476554 0.173193 2.751568 0.00593107 0.0127645
## GWK60_M14047 25.63011 -0.436302 0.694362 -0.628349 0.52977531 0.6210177
## GWK60_M14597 1.43472 1.809929 2.069943 0.874386 0.38190826 0.4805067rN = resultsNames(dds_compared_conditions_bf)
rN## [1] "Intercept" "Medium_RPMI_FLUC_vs_RPMI_DMSO"deseq_df_bf <- deseq_df_transform(dds_compared_conditions_bf,
termstokeep = rN[2])
DEGdf_up2x_FDR5_bf = get_upregulated_genes(deseq_df_bf)
DEGdf_down2x_FDR5_bf = get_downregulated_genes(deseq_df_bf)
DEGdf_non_significant_bf = get_non_significant_genes(deseq_df_bf)
write.csv(deseq_df_bf, "../data/DESeq2/BG2/BG2_FLUC_DMSO_allDESeq.csv")
p_bf = volcano_plot(deseq_df_bf, DEGdf_up2x_FDR5_bf, DEGdf_down2x_FDR5_bf,
xlabel = "log2 fold-change\n← down, FCZ up, FCZ →") +
ggtitle("FCZ vs CT, Strain BG2")
#p_bfDGE, BG2, VCZ vs CT
dds_compared_conditions_bv <-
run_deseq_vsmedium(counts_all_BG2,
conditions_to_compare = c("BG2_RPMI_DMSO", "BG2_RPMI_VORI"),
strains_to_include = "BG2")
dds_compared_conditions_bv## class: DESeqDataSet
## dim: 5234 6
## metadata(1): version
## assays(4): counts mu H cooks
## rownames(5234): GWK60_A00011 GWK60_A00033 ... GWK60_M14047 GWK60_M14597
## rowData names(22): baseMean baseVar ... deviance maxCooks
## colnames(6): BG2_RPMI_DMSO_A BG2_RPMI_VORI_A ... BG2_RPMI_DMSO_C
## BG2_RPMI_VORI_C
## colData names(10): SampleID Code ... Condition sizeFactorresults(dds_compared_conditions_bv)## log2 fold change (MLE): Medium RPMI VORI vs RPMI DMSO
## Wald test p-value: Medium RPMI VORI vs RPMI DMSO
## DataFrame with 5234 rows and 6 columns
## baseMean log2FoldChange lfcSE stat pvalue
## <numeric> <numeric> <numeric> <numeric> <numeric>
## GWK60_A00011 1.54035 0.706157 1.961312 0.360043 0.718815
## GWK60_A00033 98.51274 0.277688 0.270251 1.027519 0.304176
## GWK60_A00055 1310.77609 0.160270 0.135683 1.181213 0.237518
## GWK60_A00077 4651.26132 0.214837 0.156645 1.371487 0.170223
## GWK60_A00099 11796.21786 -0.148496 0.115114 -1.289987 0.197055
## ... ... ... ... ... ...
## GWK60_M13981 392.94428 -0.4170382 0.212398 -1.963478 0.049590615
## GWK60_M14003 205.94934 0.0780224 0.225819 0.345509 0.729711701
## GWK60_M14025 932.23403 0.5581566 0.163028 3.423687 0.000617778
## GWK60_M14047 31.46214 -0.8795011 0.645888 -1.361692 0.173295062
## GWK60_M14597 1.54035 0.7061569 1.961312 0.360043 0.718814933
## padj
## <numeric>
## GWK60_A00011 0.796081
## GWK60_A00033 0.418082
## GWK60_A00055 0.345229
## GWK60_A00077 0.263283
## GWK60_A00099 0.297058
## ... ...
## GWK60_M13981 0.09448754
## GWK60_M14003 0.80389624
## GWK60_M14025 0.00212168
## GWK60_M14047 0.26732283
## GWK60_M14597 0.79608069rN = resultsNames(dds_compared_conditions_bv)
rN## [1] "Intercept" "Medium_RPMI_VORI_vs_RPMI_DMSO"deseq_df_bv <- deseq_df_transform(dds_compared_conditions_bv,
termstokeep = rN[2])
DEGdf_up2x_FDR5_bv = get_upregulated_genes(deseq_df_bv)
DEGdf_down2x_FDR5_bv = get_downregulated_genes(deseq_df_bv)
DEGdf_non_significant_bv = get_non_significant_genes(deseq_df_bv)
write.csv(deseq_df_bv, "../data/DESeq2/BG2/BG2_VORI_DMSO_allDESeq.csv")
p_bv = volcano_plot(deseq_df_bv, DEGdf_up2x_FDR5_bv, DEGdf_down2x_FDR5_bv,
xlabel = "log2 fold-change\n← down, VCZ up, VCZ →") +
ggtitle("VCZ vs CT, Strain BG2")
#p_bvDGE, BG2, VCZ vs FCZ
dds_compared_conditions_bvf <-
run_deseq_vsmedium(counts_all_BG2,
conditions_to_compare = c("BG2_RPMI_FLUC", "BG2_RPMI_VORI"),
strains_to_include = "BG2")
dds_compared_conditions_bvf## class: DESeqDataSet
## dim: 5234 6
## metadata(1): version
## assays(4): counts mu H cooks
## rownames(5234): GWK60_A00011 GWK60_A00033 ... GWK60_M14047 GWK60_M14597
## rowData names(22): baseMean baseVar ... deviance maxCooks
## colnames(6): BG2_RPMI_VORI_A BG2_RPMI_FLUC_A ... BG2_RPMI_VORI_C
## BG2_RPMI_FLUC_C
## colData names(10): SampleID Code ... Condition sizeFactorresults(dds_compared_conditions_bvf)## log2 fold change (MLE): Medium RPMI VORI vs RPMI FLUC
## Wald test p-value: Medium RPMI VORI vs RPMI FLUC
## DataFrame with 5234 rows and 6 columns
## baseMean log2FoldChange lfcSE stat pvalue padj
## <numeric> <numeric> <numeric> <numeric> <numeric> <numeric>
## GWK60_A00011 2.37448 -2.0840627 1.927729 -1.081098 0.279654 0.99942
## GWK60_A00033 55.52361 0.3658448 0.414331 0.882977 0.377249 0.99942
## GWK60_A00055 826.42686 -0.1219869 0.183334 -0.665383 0.505806 0.99942
## GWK60_A00077 3077.75169 -0.2033374 0.172526 -1.178587 0.238562 0.99942
## GWK60_A00099 6510.95108 -0.0480715 0.131391 -0.365867 0.714464 0.99942
## ... ... ... ... ... ... ...
## GWK60_M13981 197.61007 -0.0748445 0.293316 -0.255167 0.798594 0.99942
## GWK60_M14003 134.59536 -0.2783927 0.308730 -0.901735 0.367198 0.99942
## GWK60_M14025 622.75233 0.0673620 0.173017 0.389336 0.697027 0.99942
## GWK60_M14047 15.29155 -0.4542346 0.788648 -0.575966 0.564638 0.99942
## GWK60_M14597 1.56582 -1.0663244 2.144045 -0.497342 0.618948 0.99942rN = resultsNames(dds_compared_conditions_bvf)
rN## [1] "Intercept" "Medium_RPMI_VORI_vs_RPMI_FLUC"deseq_df_bvf <- deseq_df_transform(dds_compared_conditions_bvf,
termstokeep = rN[2])
DEGdf_up2x_FDR5_bvf = get_upregulated_genes(deseq_df_bvf)
DEGdf_down2x_FDR5_bvf = get_downregulated_genes(deseq_df_bvf)
DEGdf_non_significant_bvf = get_non_significant_genes(deseq_df_bvf)
write.csv(deseq_df_bvf, "../data/DESeq2/BG2/BG2_VORI_FLUC_allDESeq.csv")
p_bvf = volcano_plot(deseq_df_bvf, DEGdf_up2x_FDR5_bvf, DEGdf_down2x_FDR5_bvf,
xlabel = "log2 fold-change\n← up, FCZ up, VCZ →") +
ggtitle("VCZ vs FCZ, Strain BG2")
# p_bvfVolcano plots of pairwise comparisons
How many genes were differentially expressed in each condition? [TODO: make it a figure]
CBS138:
## [1] "Upregulated CBS138 FCZ vs CT: 321"## [1] "Downregulated CBS138 FCZ vs CT: 409"## [1] "Upregulated in CBS138 VCZ vs CT: 338"## [1] "Downregulated in CBS138 VCZ vs CT: 353"## [1] "Upregulated in CBS138 VCZ vs FCZ: 0"## [1] "Downregulated in CBS138 VCZ vs FCZ: 0"BG2:
## [1] "Upregulated in BG2 FCZ vs CT: 271"## [1] "Downregulated in BG2 FCZ vs CT: 450"## [1] "Upregulated in BG2 VCZ vs CT: 234"## [1] "Downregulated in BG2 VCZ vs CT: 328"## [1] "Upregulated in BG2 VCZ vs FCZ: 0"## [1] "Downregulated in BG2 VCZ vs FCZ: 0"Conclusions:
- no difference between FCZ and VCZ effect in either strain.
- small but comparable number of up/downregulated genes in both strains.
- the CBS138_FLUC outlier impacts the differential expression analysis, but not in a way that changes the overall conclusions, so it is reasonable to proceed with the analysis on all 3 replicates.
Identification of corresponding genes in S. cerevisiae and between the two C.glabrata strains
Using curated orthologs between C.glabrata CBS138 and S.cerevisiae (downloaded from candidagenome.org), I identified standard and systematic S. cerevisiae names for C.glabrata genes up- and down-regulated in FCZ vs CT. There is no need to do repeat it in VCZ, because there are no significant DEG between these two conditions.
Orthologs are also identified between C.glabrata strains using Reciprocal Blast Best Hits.
Here I look at overlap between genes upregulated/downregulated in FCZ treatment between CBS138 and BG2. This includes:
- reporting the number of genes that are DE in one strain and have a homolog in the other - this shows how many genes unique for the strain are DE
- reporting the number of genes that are DE in both strain - this shows whether the response is similar between CBS138 and BG2.
## [1] "Number of FCZ upregulated genes in CBS138: 321 that have a homolog in BG2: 314"## [1] "Number of FCZ downregulated genes in CBS138: 409 that have a homolog in BG2: 405"## [1] "Number of FCZ upregulated genes in BG2: 271 that have a homolog in CBS138: 258"## [1] "Number of FCZ downregulated genes in BG2: 450 that have a homolog in CBS138: 443"## [1] "Number of FCZ upregulated genes overlapping between CBS138 and BG2: 169"## [1] "Number of FCZ downregulated genes overlapping between CBS138 and BG2: 269"Conclusions:
- most upregulated genes have homologs in both strains
- only a little more than 50% of genes differentially expressed in one strain are also differentially expressed in the other
Gene Ontology analysis of up- and down-regulated genes in CBS138 and BG2
Based on this, I used GO term enrichment (candidagenome.org) of up- and downregulated genes in CBS138, BG2 and common to both strains.
The results are in ../data/go/ folder.
Upregulated genes
Both strains up (selected):
- secondary alcohol biosynthetic process
- sterol and lipid biosynthetic process
- sulfur compound metabolic process
- secondary alcohol metabolic process
- small molecule metabolic process
- alcohol biosynthetic process
- small molecule biosynthetic process
- organic hydroxy compound biosynthetic process
- homoserine metabolic process
- non-proteinogenic amino acid metabolic process
- sulfur amino acid biosynthetic process
- aspartate family amino acid metabolic process
- amino acid import across plasma membrane
- L-methionine biosynthetic process
Only CBS138 up:
- carbohydrate metabolic process
- oligosaccharide metabolic process
- monosaccharide metabolic process
- trehalose metabolic process
BG2 only up (selected):
- lysine biosynthetic process via aminoadipic acid
- proteinogenic amino acid metabolic process
- L-amino acid metabolic process
- aspartate family amino acid biosynthetic process
Conclusions:
- both strains have upregulation of ergosterol and lipid biosynthesis genes and small molecule metabolism genes (which also includes ERG genes)
- BG2 DEG are more enriched in amino acid metabolism genes
- CBS138 are more enriched in carbohydrate metabolism genes - I think these are generally upregulated in stress?
Downregulated genes
Both strains down (selected):
- ribosome biogenes
- nucleic acid catabolism
CBS138 only:
- arginine biosynthetic process
- arginine metabolic process
- glutamine family amino acid biosynthetic process
- ornithine metabolic process
- arginine biosynthetic process via ornithine
- glutamine family amino acid metabolic process
- ribosome biogenesis
BG2 only:
- translation
- ribosome biogenesis
Conclusions:
- in both strains mostly ribosome biogenesis genes are downregulated
Comparison with transcription factor targets
Using data from two publications, both in CBS138:
I looked at differential expression of two transcription factor targets involved in antifungal resistance. This part of the analysis in CBS138 only.
This is not enrichment analysis, just search for overlapping genes.
For comparison, I’m also showing targets of S. cerevisiae homologs of these two genes (targets downloaded from SGD).
## [1] "Number of PDR1 targets in C.glabrata: 25, number of upregulated genes: 261, number of downregulated genes: 344"## [1] "Intersection UP:"## [1] "ATF2" "YOR1" "BAG7" "RTA1" "LAF1"## [1] "Intersection DOWN:"## [1] "PDR16" "RSB1"## [1] "Number of PDR1 targets in S. cerevisiae: 44, , number of upregulated genes: 261, number of downregulated genes: 344"## [1] "Intersection UP:"## [1] "GSC2" "VPS4"## [1] "Intersection DOWN:"## [1] "RPC53" "RPO26"## [1] "Number of UPC2A targets in C. glabrata: 237, , number of upregulated genes: 261, number of downregulated genes: 344"## [1] "Intersection UP:"## [1] "ERG1" "YOR1" "YOR1" "YOR1" "YOR1" "YNR014W" "YER158C"
## [8] "HEM13" "ADP1"## [1] "Intersection DOWN:"## [1] "PMA1" "PMA1" "YCL048W-A" "DSE3" "YJR115W" "TIR2"
## [7] "FUI1" "FUI1" "INA1" "INA1" "CWP1" "CWP1"
## [13] "CWP2" "CWP2" "SRP40" "PTR2" "TPO1" "YDL211C"
## [19] "SNG1" "MRH1" "RSB1" "RSB1" "GTT3" "GTT3"
## [25] "TOS1" "TOS1"## [1] "Number of UPC2 targets in S. cerevisiae: 16, , number of upregulated genes: 261, number of downregulated genes: 344"## [1] "Intersection UP:"## [1] "PRR2" "ERG25" "ERG1" "ERG11" "ERG11" "NCP1" "ERG7" "ERG3" "ERG3"
## [10] "ERG5" "ERG2"## [1] "Intersection DOWN:"## [1] "FHN1"Conclusions:
- I’m not sure how reliable this data is, for example most ERG genes do not show up among C. glabrata UPC2A targets, but do show up among S. cerevisiae Upc2; especially that the UPC2A datasets has more than 10x genes than UPC2.
- given that there is little overlap between CgPdr1 and ScPdr1 targets, I don’t know if it’s worth looking at S. cerevisiae orthologs
- using binding motifs might be a better idea.
Differential gene expression comparison between the two strains
dds_compared_conditions_cbd <-
run_deseq_vsstrain(counts_all_joined,
conditions_to_compare = c("CBS138_RPMI_DMSO", "BG2_RPMI_DMSO"))
dds_compared_conditions_cbd## class: DESeqDataSet
## dim: 5124 6
## metadata(1): version
## assays(4): counts mu H cooks
## rownames(5124): CAGL0H10626g CAGL0A00165g ... CAGL0M14069g CAGL0M14091g
## rowData names(22): baseMean baseVar ... deviance maxCooks
## colnames(6): CBS138_RPMI_DMSO_A BG2_RPMI_DMSO_A ... CBS138_RPMI_DMSO_C
## BG2_RPMI_DMSO_C
## colData names(10): SampleID Code ... Condition sizeFactorresults(dds_compared_conditions_cbd)## log2 fold change (MLE): Strain CBS138 vs BG2
## Wald test p-value: Strain CBS138 vs BG2
## DataFrame with 5124 rows and 6 columns
## baseMean log2FoldChange lfcSE stat pvalue
## <numeric> <numeric> <numeric> <numeric> <numeric>
## CAGL0H10626g 202.939 9.794973 0.873020 11.21965 3.26561e-29
## CAGL0A00165g 850.457 0.447408 0.156982 2.85006 4.37109e-03
## CAGL0A00187g 2190.078 -0.399844 0.174776 -2.28776 2.21516e-02
## CAGL0A00209g 7604.857 0.155994 0.135849 1.14829 2.50847e-01
## CAGL0A00231g 923.115 -0.712847 0.238711 -2.98623 2.82441e-03
## ... ... ... ... ... ...
## CAGL0M14003g 7912.720 0.768992 0.175128 4.39103 1.12816e-05
## CAGL0M14025g 20232.067 -0.314485 0.144817 -2.17160 2.98856e-02
## CAGL0M14047g 450.065 1.261566 0.246975 5.10807 3.25462e-07
## CAGL0M14069g 145.683 0.579965 0.290451 1.99677 4.58500e-02
## CAGL0M14091g 621.588 0.883936 0.191359 4.61924 3.85141e-06
## padj
## <numeric>
## CAGL0H10626g 4.30365e-27
## CAGL0A00165g 1.77195e-02
## CAGL0A00187g 6.63057e-02
## CAGL0A00209g 4.08304e-01
## CAGL0A00231g 1.24622e-02
## ... ...
## CAGL0M14003g 1.08490e-04
## CAGL0M14025g 8.27750e-02
## CAGL0M14047g 4.53170e-06
## CAGL0M14069g 1.15846e-01
## CAGL0M14091g 4.08585e-05rN = resultsNames(dds_compared_conditions_cbd)
rN## [1] "Intercept" "Strain_CBS138_vs_BG2"deseq_df_cbd <- deseq_df_transform(dds_compared_conditions_cbd,
termstokeep = rN[2])
write.csv(deseq_df_cbd, "../data/DESeq2/CompareStrains/CBS138_BG2_DMSO_allDESeq.csv")
DEGdf_up2x_FDR5_cbd = get_upregulated_genes(deseq_df_cbd)
DEGdf_down2x_FDR5_cbd = get_downregulated_genes(deseq_df_cbd)
DEGdf_non_significant_cbd = get_non_significant_genes(deseq_df_cbd)
print(DEGdf_up2x_FDR5_cbd, n = 20)## # A tibble: 194 × 5
## gene baseMean log2FC stderror padj
## <chr> <dbl> <dbl> <dbl> <dbl>
## 1 CAGL0K00110g 13966. 12.5 0.809 3.70e- 51
## 2 CAGL0C00110g 4327. 10.3 0.274 1.58e-303
## 3 CAGL0H10626g 203. 9.79 0.873 4.30e- 27
## 4 CAGL0E00187g 550. 8.81 0.816 3.86e- 25
## 5 CAGL0E06666g 2836. 8.68 0.823 6.27e- 24
## 6 CAGL0K13024g 1275. 8.65 0.334 9.32e-145
## 7 CAGL0B00264g 69.1 7.83 0.803 1.63e- 20
## 8 CAGL0M00132g 49.9 6.75 0.736 3.45e- 18
## 9 CAGL0G10219g 52.1 5.84 1.52 8.46e- 4
## 10 CAGL0I00220g 17.2 4.77 0.833 1.91e- 7
## 11 CAGL0A01221g 9209. 4.71 0.163 1.59e-179
## 12 CAGL0D06534g 7.72 4.60 1.08 1.82e- 4
## 13 CAGL0E00275g 178. 4.56 0.312 4.70e- 46
## 14 CAGL0B00990g 7455. 4.51 0.226 6.87e- 86
## 15 CAGL0J11891g 19.9 4.25 0.693 1.89e- 8
## 16 CAGL0H06039g 107. 4.19 0.446 4.61e- 19
## 17 CAGL0M11044g 4.25 4.15 1.41 1.37e- 2
## 18 CAGL0M13387g 4.19 4.12 1.52 2.49e- 2
## 19 CAGL0C00781g 4.06 4.07 1.37 1.26e- 2
## 20 CAGL0F08217g 101. 3.89 0.492 1.34e- 13
## # ℹ 174 more rowsprint(DEGdf_down2x_FDR5_cbd, n = 20)## # A tibble: 265 × 5
## gene baseMean log2FC stderror padj
## <chr> <dbl> <dbl> <dbl> <dbl>
## 1 CAGL0A02233g 11597. -9.06 0.584 1.08e- 51
## 2 CAGL0J11550g 3730. -7.13 0.300 4.86e-122
## 3 CAGL0C00209g 56.8 -5.71 0.898 5.05e- 9
## 4 CAGL0H04279g 42.6 -5.28 0.904 9.96e- 8
## 5 CAGL0H02563g 3100. -5.20 0.237 1.27e-103
## 6 CAGL0K00407g 2119. -4.55 0.234 6.80e- 82
## 7 CAGL0B01232g 2758. -4.28 0.209 1.85e- 90
## 8 CAGL0A01826g 1997. -4.21 0.640 1.24e- 9
## 9 CAGL0E05984g 979. -4.15 0.276 1.41e- 48
## 10 CAGL0I06336g 558. -3.78 0.234 5.22e- 56
## 11 CAGL0G02937g 50.6 -3.66 0.617 6.05e- 8
## 12 CAGL0G01738g 4149. -3.63 0.168 2.13e-101
## 13 CAGL0F06677g 13.5 -3.53 1.04 3.72e- 3
## 14 CAGL0J04004g 1049. -3.48 0.248 2.15e- 42
## 15 CAGL0D02244g 22.3 -3.44 0.881 6.75e- 4
## 16 CAGL0K04565g 123. -3.33 0.384 2.77e- 16
## 17 CAGL0L05434g 6247. -3.24 0.198 1.62e- 57
## 18 CAGL0K08932g 462. -3.24 0.273 3.13e- 30
## 19 CAGL0J03080g 2302. -3.11 0.270 1.44e- 28
## 20 CAGL0F05137g 103. -3.10 0.423 8.22e- 12
## # ℹ 245 more rowsprint(DEGdf_non_significant_cbd, n = 20)## # A tibble: 3,717 × 5
## gene baseMean log2FC stderror padj
## <chr> <dbl> <dbl> <dbl> <dbl>
## 1 CAGL0L06578g 7.72 -2.61 1.31 0.118
## 2 CAGL0B00220g 5.40 -1.99 1.19 0.201
## 3 CAGL0F08261g 12958. -1.98 0.870 0.0674
## 4 CAGL0D01694g 13.6 -1.86 0.854 0.0817
## 5 CAGL0M12771g 4.81 -1.77 1.26 0.299
## 6 CAGL0A03410g 13.9 -1.76 0.765 0.0645
## 7 CAGL0G02849g 1120. -1.66 0.906 0.155
## 8 CAGL0H00352g 17.0 -1.65 0.794 0.0999
## 9 CAGL0H03135g 17.9 -1.49 0.838 0.169
## 10 CAGL0M08580g 20.5 -1.46 0.729 0.113
## 11 CAGL0K08074g 4.10 -1.45 1.42 0.466
## 12 CAGL0G00792g 4.04 -1.43 1.30 0.431
## 13 CAGL0A03806g 3.98 -1.39 1.72 0.583
## 14 CAGL0M01980g 8.99 -1.35 1.00 0.319
## 15 CAGL0F04631g 591. -1.34 1.23 0.435
## 16 CAGL0E01727g 4797. -1.33 0.611 0.0821
## 17 CAGL0F05093g 21.2 -1.31 0.702 0.148
## 18 CAGL0L02739g 10.5 -1.29 0.979 0.333
## 19 CAGL0J06028g 2092. -1.26 0.633 0.117
## 20 CAGL0M02343g 21.4 -1.21 0.683 0.171
## # ℹ 3,697 more rowswrite.csv(DEGdf_up2x_FDR5_cbd, "../data/DESeq2/CompareStrains/CBS138_BG2_DMSO_up2x_FDR5.csv")
writeLines(DEGdf_up2x_FDR5_cbd$gene, "../data/DESeq2/CompareStrains/CBS138_BG2_DMSO_up2x_FDR5_names.txt")
write.csv(DEGdf_down2x_FDR5_cbd, "../data/DESeq2/CompareStrains/CBS138_BG2_DMSO_down2x_FDR5.csv")
writeLines(DEGdf_down2x_FDR5_cbd$gene, "../data/DESeq2/CompareStrains/CBS138_BG2_DMSO_down2x_FDR5_names.txt")
p_cbd = volcano_plot(deseq_df_cbd, DEGdf_up2x_FDR5_cbd, DEGdf_down2x_FDR5_cbd,
xlabel = "log2 fold-change\nup, BG2 up, CBS138\n← →") +
ggtitle("Strain BG2 vs CBS138\nin RPMI CT")
#p_cbd
print("Upregulated genes:")## [1] "Upregulated genes:"nrow(DEGdf_up2x_FDR5_cbd)## [1] 194print("Downregulated genes")## [1] "Downregulated genes"nrow(DEGdf_down2x_FDR5_cbd)## [1] 265dds_compared_conditions_cbv <-
run_deseq_vsstrain(counts_all_joined,
conditions_to_compare = c("CBS138_RPMI_VORI", "BG2_RPMI_VORI"))
dds_compared_conditions_cbv## class: DESeqDataSet
## dim: 5124 6
## metadata(1): version
## assays(4): counts mu H cooks
## rownames(5124): CAGL0H10626g CAGL0A00165g ... CAGL0M14069g CAGL0M14091g
## rowData names(22): baseMean baseVar ... deviance maxCooks
## colnames(6): CBS138_RPMI_VORI_A BG2_RPMI_VORI_A ... CBS138_RPMI_VORI_C
## BG2_RPMI_VORI_C
## colData names(10): SampleID Code ... Condition sizeFactorresults(dds_compared_conditions_cbv)## log2 fold change (MLE): Strain CBS138 vs BG2
## Wald test p-value: Strain CBS138 vs BG2
## DataFrame with 5124 rows and 6 columns
## baseMean log2FoldChange lfcSE stat pvalue
## <numeric> <numeric> <numeric> <numeric> <numeric>
## CAGL0H10626g 197.928 9.6176284 1.001505 9.6031748 7.75192e-22
## CAGL0A00165g 964.438 0.8215197 0.234334 3.5057649 4.55297e-04
## CAGL0A00187g 2374.245 -0.1850700 0.347642 -0.5323578 5.94478e-01
## CAGL0A00209g 5795.186 0.0759132 0.302842 0.2506697 8.02070e-01
## CAGL0A00231g 298.234 -0.0204449 0.444757 -0.0459686 9.63335e-01
## ... ... ... ... ... ...
## CAGL0M14003g 12219.286 1.227250 0.315691 3.88750 0.000101281
## CAGL0M14025g 16734.160 -0.438702 0.215256 -2.03805 0.041545417
## CAGL0M14047g 309.375 1.437608 0.590298 2.43539 0.014875631
## CAGL0M14069g 142.758 0.738347 0.317943 2.32226 0.020218906
## CAGL0M14091g 846.220 1.013221 0.231136 4.38366 0.000011670
## padj
## <numeric>
## CAGL0H10626g 2.20542e-19
## CAGL0A00165g 6.66165e-03
## CAGL0A00187g 7.89708e-01
## CAGL0A00209g 9.09735e-01
## CAGL0A00231g 9.86629e-01
## ... ...
## CAGL0M14003g 0.001845771
## CAGL0M14025g 0.174818472
## CAGL0M14047g 0.093013561
## CAGL0M14069g 0.113458022
## CAGL0M14091g 0.000312297rN = resultsNames(dds_compared_conditions_cbv)
rN## [1] "Intercept" "Strain_CBS138_vs_BG2"deseq_df_cbv <- deseq_df_transform(dds_compared_conditions_cbv,
termstokeep = rN[2])
write.csv(deseq_df_cbv, "../data/DESeq2/CompareStrains/CBS138_BG2_VORI_allDESeq.csv")
DEGdf_up2x_FDR5_cbv = get_upregulated_genes(deseq_df_cbv)
DEGdf_down2x_FDR5_cbv = get_downregulated_genes(deseq_df_cbv)
DEGdf_non_significant_cbv = get_non_significant_genes(deseq_df_cbv)
print(DEGdf_up2x_FDR5_cbv, n = 20)## # A tibble: 187 × 5
## gene baseMean log2FC stderror padj
## <chr> <dbl> <dbl> <dbl> <dbl>
## 1 CAGL0E00187g 2272. 11.3 0.742 1.85e-49
## 2 CAGL0K00110g 4669. 10.9 0.773 1.24e-42
## 3 CAGL0H10626g 198. 9.62 1.00 2.21e-19
## 4 CAGL0E06666g 3341. 9.55 0.461 8.39e-92
## 5 CAGL0C00110g 2533. 9.24 0.472 4.53e-82
## 6 CAGL0K13024g 1352. 8.93 0.442 2.46e-87
## 7 CAGL0M00132g 60.8 6.19 0.776 2.94e-13
## 8 CAGL0H09922g 16.8 5.78 1.41 9.10e- 4
## 9 CAGL0I00220g 40.9 5.72 0.820 3.55e-10
## 10 CAGL0B00264g 92.1 5.64 1.08 7.65e- 6
## 11 CAGL0L05984g 207. 5.62 0.387 5.33e-45
## 12 CAGL0D06468g 30.4 4.52 1.21 3.24e- 3
## 13 CAGL0E00275g 127. 4.23 0.557 5.47e-12
## 14 CAGL0A01221g 3954. 4.18 0.476 3.22e-16
## 15 CAGL0B00990g 3957. 4.10 0.270 4.66e-49
## 16 CAGL0G10175g 7.10 4.05 1.46 4.64e- 2
## 17 CAGL0I09856g 1402. 3.96 0.319 6.71e-33
## 18 CAGL0D06534g 8.72 3.93 1.28 2.22e- 2
## 19 CAGL0G10219g 26.2 3.90 1.25 2.02e- 2
## 20 CAGL0G06798g 266. 3.90 0.478 7.27e-14
## # ℹ 167 more rowsprint(DEGdf_down2x_FDR5_cbv, n = 20)## # A tibble: 256 × 5
## gene baseMean log2FC stderror padj
## <chr> <dbl> <dbl> <dbl> <dbl>
## 1 CAGL0A02233g 7253. -9.15 0.473 2.99e-80
## 2 CAGL0J11550g 8046. -8.02 0.510 8.79e-53
## 3 CAGL0C00209g 137. -5.71 0.577 1.52e-20
## 4 CAGL0M03305g 271. -4.79 0.726 4.43e- 9
## 5 CAGL0K00407g 1811. -4.41 0.294 3.75e-48
## 6 CAGL0G02937g 35.6 -4.39 0.970 1.76e- 4
## 7 CAGL0H04279g 22.9 -4.20 0.962 3.26e- 4
## 8 CAGL0E05984g 3078. -4.15 0.780 5.12e- 6
## 9 CAGL0K10164g 7452. -4.08 0.680 1.51e- 7
## 10 CAGL0H02563g 2350. -4.07 0.629 9.58e- 9
## 11 CAGL0G01738g 4511. -4.06 0.346 3.15e-29
## 12 CAGL0H10076g 37.2 -4.06 0.773 7.35e- 6
## 13 CAGL0B01232g 1831. -3.72 0.710 7.47e- 6
## 14 CAGL0K08932g 528. -3.53 0.806 3.12e- 4
## 15 CAGL0I02838g 810. -3.51 0.659 5.08e- 6
## 16 CAGL0C03740g 1012. -3.44 0.361 5.00e-19
## 17 CAGL0F05137g 71.4 -3.42 0.607 1.08e- 6
## 18 CAGL0F08261g 7875. -3.29 0.439 9.80e-12
## 19 CAGL0K04565g 61.2 -3.27 0.939 7.07e- 3
## 20 CAGL0M03465g 218. -3.26 0.705 1.13e- 4
## # ℹ 236 more rowsprint(DEGdf_non_significant_cbv, n = 20)## # A tibble: 4,668 × 5
## gene baseMean log2FC stderror padj
## <chr> <dbl> <dbl> <dbl> <dbl>
## 1 CAGL0M12056g 15.2 -2.70 1.01 0.0579
## 2 CAGL0C02629g 7.97 -2.67 1.42 0.220
## 3 CAGL0F08701g 9.22 -2.66 1.18 0.124
## 4 CAGL0G00792g 9.11 -2.59 1.28 0.178
## 5 CAGL0H03135g 9.36 -2.30 1.22 0.218
## 6 CAGL0M12100g 7.49 -2.27 1.59 0.381
## 7 CAGL0M03377g 1651. -2.09 0.786 0.0579
## 8 CAGL0F04521g 31.9 -2.00 0.904 0.134
## 9 CAGL0I04664g 26.0 -1.99 0.818 0.0931
## 10 CAGL0G07755g 8.08 -1.98 1.18 0.287
## 11 CAGL0J07348g 72.8 -1.97 0.893 0.135
## 12 CAGL0G03729g 13.6 -1.96 0.977 0.182
## 13 CAGL0H06325g 24.0 -1.96 0.932 0.156
## 14 CAGL0I07051g 547. -1.94 0.872 0.131
## 15 CAGL0D05720g 4.16 -1.93 1.82 0.546
## 16 CAGL0J11616g 12.4 -1.91 1.39 0.403
## 17 CAGL0J00363g 17.0 -1.89 0.986 0.208
## 18 CAGL0I00726g 3.64 -1.89 1.62 0.497
## 19 CAGL0H00352g 13.6 -1.88 0.863 0.139
## 20 CAGL0G05335g 2090. -1.85 0.688 0.0542
## # ℹ 4,648 more rowsp_cbv = volcano_plot(deseq_df_cbv, DEGdf_up2x_FDR5_cbv, DEGdf_down2x_FDR5_cbv,
xlabel = "log2 fold-change\n← up, BG2 up, CBS138 →") +
ggtitle("Strain comparison in RPMI VCZ")
#p_cbv
print("Upregulated genes:")## [1] "Upregulated genes:"nrow(DEGdf_up2x_FDR5_cbv)## [1] 187print("Downregulated genes")## [1] "Downregulated genes"nrow(DEGdf_down2x_FDR5_cbv)## [1] 256dds_compared_conditions_cbf <-
run_deseq_vsstrain(counts_all_joined,
conditions_to_compare = c("CBS138_RPMI_FLUC", "BG2_RPMI_FLUC"))
dds_compared_conditions_cbf## class: DESeqDataSet
## dim: 5124 6
## metadata(1): version
## assays(4): counts mu H cooks
## rownames(5124): CAGL0H10626g CAGL0A00165g ... CAGL0M14069g CAGL0M14091g
## rowData names(22): baseMean baseVar ... deviance maxCooks
## colnames(6): CBS138_RPMI_FLUC_A BG2_RPMI_FLUC_A ... CBS138_RPMI_FLUC_C
## BG2_RPMI_FLUC_C
## colData names(10): SampleID Code ... Condition sizeFactorresults(dds_compared_conditions_cbf)## log2 fold change (MLE): Strain CBS138 vs BG2
## Wald test p-value: Strain CBS138 vs BG2
## DataFrame with 5124 rows and 6 columns
## baseMean log2FoldChange lfcSE stat pvalue
## <numeric> <numeric> <numeric> <numeric> <numeric>
## CAGL0H10626g 259.989 7.689615 1.049868 7.32436 2.40033e-13
## CAGL0A00165g 995.133 0.489868 0.169866 2.88385 3.92852e-03
## CAGL0A00187g 2675.261 -0.525863 0.155620 -3.37915 7.27105e-04
## CAGL0A00209g 7023.453 0.274270 0.150235 1.82561 6.79097e-02
## CAGL0A00231g 371.162 0.281902 0.249171 1.13136 2.57903e-01
## ... ... ... ... ... ...
## CAGL0M14003g 10105.213 0.696847 0.137365 5.07296 3.91666e-07
## CAGL0M14025g 17658.342 -0.535564 0.127272 -4.20803 2.57611e-05
## CAGL0M14047g 573.991 2.299193 0.230542 9.97299 2.00106e-23
## CAGL0M14069g 182.854 0.666365 0.291378 2.28695 2.21990e-02
## CAGL0M14091g 870.946 0.992741 0.164226 6.04498 1.49425e-09
## padj
## <numeric>
## CAGL0H10626g 6.83160e-12
## CAGL0A00165g 1.50642e-02
## CAGL0A00187g 3.65909e-03
## CAGL0A00209g 1.47316e-01
## CAGL0A00231g 4.01141e-01
## ... ...
## CAGL0M14003g 4.32437e-06
## CAGL0M14025g 1.89003e-04
## CAGL0M14047g 1.28143e-21
## CAGL0M14069g 6.14732e-02
## CAGL0M14091g 2.46937e-08rN = resultsNames(dds_compared_conditions_cbf)
rN## [1] "Intercept" "Strain_CBS138_vs_BG2"deseq_df_cbf <- deseq_df_transform(dds_compared_conditions_cbf,
termstokeep = rN[2])
write.csv(deseq_df_cbf, "../data/DESeq2/CompareStrains/CBS138_BG2_FLUC_allDESeq.csv")
DEGdf_up2x_FDR5_cbf = get_upregulated_genes(deseq_df_cbf)
DEGdf_down2x_FDR5_cbf = get_downregulated_genes(deseq_df_cbf)
DEGdf_non_significant_cbf = get_non_significant_genes(deseq_df_cbf)
print(DEGdf_up2x_FDR5_cbf, n = 20)## # A tibble: 184 × 5
## gene baseMean log2FC stderror padj
## <chr> <dbl> <dbl> <dbl> <dbl>
## 1 CAGL0K00110g 9811. 10.4 1.21 3.51e- 16
## 2 CAGL0E00187g 2002. 10.3 0.754 4.96e- 40
## 3 CAGL0E06666g 3643. 8.84 1.19 3.86e- 12
## 4 CAGL0K13024g 1368. 8.40 0.344 3.37e-128
## 5 CAGL0H10626g 260. 7.69 1.05 6.83e- 12
## 6 CAGL0C00110g 3068. 7.43 0.783 1.26e- 19
## 7 CAGL0B00264g 101. 7.02 0.723 1.44e- 20
## 8 CAGL0I00220g 34.4 6.05 0.944 2.98e- 9
## 9 CAGL0M00132g 91.8 5.76 0.568 2.85e- 22
## 10 CAGL0H06039g 70.9 4.96 0.553 1.49e- 17
## 11 CAGL0J11891g 12.4 4.32 1.15 1.02e- 3
## 12 CAGL0A01221g 5692. 4.30 0.146 5.26e-188
## 13 CAGL0E00275g 121. 4.23 0.393 5.05e- 25
## 14 CAGL0H09922g 14.0 4.21 1.05 3.98e- 4
## 15 CAGL0L06072g 51.9 4.03 0.616 1.34e- 9
## 16 CAGL0L05984g 227. 3.95 0.295 1.44e- 38
## 17 CAGL0F00209g 38.5 3.90 0.629 9.73e- 9
## 18 CAGL0D06534g 9.01 3.74 1.21 8.75e- 3
## 19 CAGL0E03894g 562. 3.66 0.259 6.89e- 43
## 20 CAGL0M00308g 67.6 3.60 0.493 7.72e- 12
## # ℹ 164 more rowsprint(DEGdf_down2x_FDR5_cbf, n = 20)## # A tibble: 242 × 5
## gene baseMean log2FC stderror padj
## <chr> <dbl> <dbl> <dbl> <dbl>
## 1 CAGL0A02233g 7338. -8.53 1.01 1.26e- 15
## 2 CAGL0J11550g 10582. -8.01 0.218 1.69e-290
## 3 CAGL0C00209g 161. -5.70 0.392 1.73e- 45
## 4 CAGL0H04279g 15.0 -4.82 1.05 3.92e- 5
## 5 CAGL0H03135g 11.1 -4.28 1.03 2.40e- 4
## 6 CAGL0B01232g 1831. -4.13 0.184 5.41e-108
## 7 CAGL0M03305g 362. -4.06 0.307 9.26e- 38
## 8 CAGL0F06677g 17.7 -4.03 0.879 4.03e- 5
## 9 CAGL0K00407g 1931. -3.93 0.465 1.16e- 15
## 10 CAGL0C03872g 15011. -3.64 0.158 4.49e-115
## 11 CAGL0G01738g 4948. -3.60 0.187 5.78e- 80
## 12 CAGL0C03740g 1086. -3.46 0.193 5.54e- 69
## 13 CAGL0D02244g 22.5 -3.12 0.699 6.66e- 5
## 14 CAGL0H10076g 38.1 -3.09 0.531 8.91e- 8
## 15 CAGL0I02838g 865. -3.08 0.189 1.77e- 57
## 16 CAGL0L06996g 80.8 -3.00 0.381 1.01e- 13
## 17 CAGL0B00220g 17.1 -2.96 0.945 7.76e- 3
## 18 CAGL0J03080g 7456. -2.94 0.194 3.42e- 49
## 19 CAGL0F08261g 12221. -2.93 0.183 5.88e- 55
## 20 CAGL0K10164g 9075. -2.91 0.147 2.54e- 84
## # ℹ 222 more rowsprint(DEGdf_non_significant_cbf, n = 20)## # A tibble: 3,542 × 5
## gene baseMean log2FC stderror padj
## <chr> <dbl> <dbl> <dbl> <dbl>
## 1 CAGL0H07073g 3.42 -3.04 1.60 0.129
## 2 CAGL0L04832g 5.03 -2.71 1.27 0.0846
## 3 CAGL0H04015g 2.57 -2.54 1.75 0.263
## 4 CAGL0L05830g 3.37 -2.33 1.54 0.239
## 5 CAGL0K12540g 2.10 -2.15 1.85 0.386
## 6 CAGL0M00726g 10.4 -1.88 0.954 0.116
## 7 CAGL0G00792g 10.4 -1.74 0.939 0.140
## 8 CAGL0M04851g 1.70 -1.68 1.98 0.541
## 9 CAGL0G03993g 5.32 -1.66 1.18 0.281
## 10 CAGL0K08074g 3.11 -1.65 1.57 0.437
## 11 CAGL0J02046g 1.79 -1.64 1.99 0.557
## 12 CAGL0M04103g 4.34 -1.59 1.37 0.384
## 13 CAGL0L03894g 16.9 -1.57 0.780 0.105
## 14 CAGL0H08217g 12.4 -1.47 0.890 0.195
## 15 CAGL0J08932g 11.8 -1.44 0.862 0.190
## 16 CAGL0L06336g 2.57 -1.44 1.64 0.529
## 17 CAGL0G01408g 19.5 -1.43 0.662 0.0802
## 18 CAGL0M12056g 14.4 -1.39 0.731 0.127
## 19 CAGL0C02629g 4.93 -1.38 1.27 0.422
## 20 CAGL0J10868g 3.16 -1.35 1.50 0.513
## # ℹ 3,522 more rowsp_cbf = volcano_plot(deseq_df_cbf, DEGdf_up2x_FDR5_cbf, DEGdf_down2x_FDR5_cbf,
xlabel = "log2 fold-change\n← up, BG2 up, CBS138 →") +
ggtitle("Strain comparison in RPMI FCZ")
#p_cbf
print("Upregulated genes:")## [1] "Upregulated genes:"nrow(DEGdf_up2x_FDR5_cbf)## [1] 184print("Downregulated genes")## [1] "Downregulated genes"nrow(DEGdf_down2x_FDR5_cbf)## [1] 242
Report number of differentially expressed genes in CBS138 vs BG2:
## [1] "CT upregulated: 194, downregulated: 265"## [1] "FCZ upregulated: 184, downregulated: 242"## [1] "VCZ upregulated: 187, downregulated: 256"GO analysis of strain differences
CT upregulated in CBS138 (selected):
- amino acid biosynthesis
- cell adhesion
- spore wall assembly
- cell wall assembly
CT downregulated in CBS138 (selected):
- trehalose metabolism
- small molecule catabolism
- lipid catabolism
FCZ upregulated in CBS138:
- cell adhesion: AWP2, CAGL0A01584g, CAGL0I09856g, CAGL0K12078g, EPA23, EPA6
FCZ downregulated in CBS138 (selected):
- small molecule catabolism
- energy derivation by oxidation of organic compounds
VCZ upregulated in CBS138:
- cell adhesion: AWP2, CAGL0A01584g, CAGL0I09856g, EPA23, EPA3, EPA6
- filamentous growth: CAGL0H02145g, CAGL0I01254g, CAGL0I09856g, CAGL0K04169g, CAGL0M03663g, CAGL0M09042g, EFG1, SHO1, TEC1, YPS2
VCZ downregulated in CBS138:
- small molecule catabolism
- trehalose metabolism
- carbohydrate metabolism
- energy derivation by oxidation of organic compounds
Analysis of Drug vs no Drug and strain differences
The above conclusions for pairwise comparisons suggest that we should compare:
- Drug vs no drug, taking average of VCZ and FCZ responses
- and compare across strains to get the strain-specific drug interactions
Differential expression shared across both strains, both drugs
Here, “up” means that both drugs induces more transcript abundance in both strains. Essentially, treating both drugs as biological replicates, and both strains as biological replicates.
sample_sheet_all_drugnodrug <-
sample_sheet_all %>%
# select only relevant columns
dplyr::select(SampleID, Code, Strain, Medium, Rep) %>%
# make Strain a factor in predictable order
mutate(Strain = factor(Strain,
levels = c("BG2", "CBS138"))
) %>%
# create two new columns for Drug, and Voriconazole vs Fluconazole
mutate(Drug = Medium %in% c("RPMI_FLUC", "RPMI_VORI"),
VORI = Medium %in% c("RPMI_VORI")) %>%
magrittr::set_rownames(.$Code)## Warning: Setting row names on a tibble is deprecated.dds_drugnodrug_bc <-
DESeqDataSetFromMatrix(
countData = counts_all_joined %>%
dplyr::select(sample_sheet_all_drugnodrug$Code) %>%
magrittr::set_rownames(counts_all_joined$Gene),
colData = sample_sheet_all_drugnodrug,
design = ~ Strain + Drug) %>%
DESeq()## estimating size factors## estimating dispersions## gene-wise dispersion estimates## mean-dispersion relationship## final dispersion estimates## fitting model and testingresultsNames(dds_drugnodrug_bc)## [1] "Intercept" "Strain_CBS138_vs_BG2" "DrugTRUE"deseq_df_drugnodrug_bc <-
deseq_df_transform(dds_drugnodrug_bc,
termstokeep = "DrugTRUE")
deseq_df_drugnodrug_bc## # A tibble: 5,124 × 5
## gene baseMean log2FC stderror padj
## <chr> <dbl> <dbl> <dbl> <dbl>
## 1 CAGL0H10626g 220. 0.429 0.363 0.324
## 2 CAGL0A00165g 939. 0.333 0.0975 0.00167
## 3 CAGL0A00187g 2413. 0.358 0.136 0.0174
## 4 CAGL0A00209g 6755. -0.0959 0.115 0.501
## 5 CAGL0A00231g 515. -1.29 0.218 0.0000000196
## 6 CAGL0A00253g 2282. 0.0481 0.133 0.787
## 7 CAGL0A00275g 2973. -0.196 0.140 0.234
## 8 CAGL0A00297g 1698. 0.0577 0.115 0.699
## 9 CAGL0A00319g 1804. 0.418 0.0855 0.00000436
## 10 CAGL0A00341g 654. 0.883 0.205 0.0000584
## # ℹ 5,114 more rowsDEGdf_up2x_FDR5_drug = get_upregulated_genes(deseq_df_drugnodrug_bc)
DEGdf_down2x_FDR5_drug = get_downregulated_genes(deseq_df_drugnodrug_bc)
print(DEGdf_up2x_FDR5_drug, n = 20)## # A tibble: 258 × 5
## gene baseMean log2FC stderror padj
## <chr> <dbl> <dbl> <dbl> <dbl>
## 1 CAGL0A01089g 24754. 4.34 0.148 2.89e-185
## 2 CAGL0J03916g 8684. 3.88 0.169 1.56e-113
## 3 CAGL0L06094g 4710. 3.65 0.191 2.78e- 78
## 4 CAGL0F03641g 7427. 3.54 0.304 1.47e- 29
## 5 CAGL0K08668g 1429. 3.52 0.180 4.47e- 82
## 6 CAGL0D05940g 23664. 3.05 0.170 1.49e- 69
## 7 CAGL0M03839g 21921. 2.99 0.199 1.15e- 48
## 8 CAGL0B02838g 7089. 2.93 0.220 1.99e- 38
## 9 CAGL0F07029g 3902. 2.85 0.209 1.92e- 40
## 10 CAGL0B03663g 5540. 2.60 0.181 1.32e- 44
## 11 CAGL0M07403g 2557. 2.57 0.162 2.99e- 54
## 12 CAGL0M01760g 15392. 2.51 0.220 1.80e- 28
## 13 CAGL0D01474g 1672. 2.51 0.211 8.67e- 31
## 14 CAGL0C03872g 10721. 2.50 0.266 1.81e- 19
## 15 CAGL0K06677g 840. 2.45 0.195 2.91e- 34
## 16 CAGL0L06776g 1896. 2.44 0.206 1.96e- 30
## 17 CAGL0J04158g 13362. 2.43 0.202 1.85e- 31
## 18 CAGL0I05610g 6319. 2.40 0.205 9.53e- 30
## 19 CAGL0E05984g 2581. 2.38 0.479 3.07e- 6
## 20 CAGL0K10824g 1318. 2.36 0.193 3.33e- 32
## # ℹ 238 more rowsprint(DEGdf_down2x_FDR5_drug, n = 20)## # A tibble: 355 × 5
## gene baseMean log2FC stderror padj
## <chr> <dbl> <dbl> <dbl> <dbl>
## 1 CAGL0H10076g 136. -3.43 0.287 4.70e-31
## 2 CAGL0E02255g 1670. -3.08 0.346 1.02e-17
## 3 CAGL0H08712g 114. -2.84 0.285 6.21e-22
## 4 CAGL0L10142g 132. -2.80 0.281 8.07e-22
## 5 CAGL0M03305g 627. -2.78 0.500 1.45e- 7
## 6 CAGL0L01551g 1556. -2.69 0.198 4.96e-40
## 7 CAGL0J05390g 208. -2.46 0.384 1.07e- 9
## 8 CAGL0L13156g 229. -2.25 0.261 1.10e-16
## 9 CAGL0B00792g 252. -2.21 0.239 4.93e-19
## 10 CAGL0C02211g 674. -2.21 0.217 9.15e-23
## 11 CAGL0K06259g 3403. -2.19 0.306 8.23e-12
## 12 CAGL0K00605g 272. -2.14 0.221 8.31e-21
## 13 CAGL0G03927g 99.4 -2.03 0.225 4.15e-18
## 14 CAGL0I09592g 938. -1.93 0.288 1.89e-10
## 15 CAGL0F01463g 108605. -1.90 0.281 1.19e-10
## 16 CAGL0D04620g 213. -1.89 0.307 5.18e- 9
## 17 CAGL0F05709g 138. -1.88 0.322 3.33e- 8
## 18 CAGL0L10890g 2359. -1.87 0.212 2.38e-17
## 19 CAGL0C01749g 1326. -1.85 0.162 1.86e-28
## 20 CAGL0G05742g 1416. -1.83 0.141 1.14e-36
## # ℹ 335 more rowsp_drugnodrug_bc =
volcano_plot(deseq_df_drugnodrug_bc,
DEGdf_up2x_FDR5_drug,
DEGdf_down2x_FDR5_drug,
xlabel = "log2 fold-change\ndown, azole up, azole\n← →") +
ggtitle("Azole vs CT\n across both strains")
p_drugnodrug_bc## Warning: Removed 16 rows containing missing values or values outside the scale range
## (`geom_point()`).
write.csv(deseq_df_drugnodrug_bc, "../data/DESeq2/DrugBothStrains/BothStrains_Drug_vs_DMSO_allDESeq.csv")
write.csv(DEGdf_up2x_FDR5_drug, "../data/DESeq2/DrugBothStrains/BothStrains_Drug_vs_DMSO_up2x_FDR5.csv")
writeLines(DEGdf_up2x_FDR5_drug$gene, "../data/DESeq2/DrugBothStrains/BothStrains_Drug_vs_DMSO_up2x_FDR5_names.txt")
write.csv(DEGdf_down2x_FDR5_drug, "../data/DESeq2/DrugBothStrains/BothStrains_Drug_vs_DMSO_down2x_FDR5.csv")
writeLines(DEGdf_down2x_FDR5_drug$gene, "../data/DESeq2/DrugBothStrains/BothStrains_Drug_vs_DMSO_down2x_FDR5_names.txt")Differential drug-strain interactions across strains
We’re looking for differential strain responses to drug. Here, “up” means that azoles induce more change in transcript abundance in CBS138 as compared to BG2. Again, treating both drugs as biological replicates, due to the small differences in response to the two diferent drugs.
dds_drugstrain <-
DESeqDataSetFromMatrix(
countData = counts_all_joined %>%
dplyr::select(sample_sheet_all_drugnodrug$Code) %>%
magrittr::set_rownames(counts_all_joined$Gene),
colData = sample_sheet_all_drugnodrug,
design = ~ Strain * Drug) %>%
DESeq()## estimating size factors## estimating dispersions## gene-wise dispersion estimates## mean-dispersion relationship## final dispersion estimates## fitting model and testingresultsNames(dds_drugstrain)## [1] "Intercept" "Strain_CBS138_vs_BG2" "DrugTRUE"
## [4] "StrainCBS138.DrugTRUE"deseq_df_drugstrain <-
deseq_df_transform(dds_drugstrain,
termstokeep = "StrainCBS138.DrugTRUE")
deseq_df_drugstrain## # A tibble: 5,124 × 5
## gene baseMean log2FC stderror padj
## <chr> <dbl> <dbl> <dbl> <dbl>
## 1 CAGL0H10626g 220. -0.916 1.18 0.986
## 2 CAGL0A00165g 939. 0.220 0.192 0.986
## 3 CAGL0A00187g 2413. 0.0531 0.279 0.991
## 4 CAGL0A00209g 6755. 0.0379 0.237 0.991
## 5 CAGL0A00231g 515. 0.865 0.399 0.546
## 6 CAGL0A00253g 2282. 0.0776 0.273 0.991
## 7 CAGL0A00275g 2973. 0.0260 0.288 0.993
## 8 CAGL0A00297g 1698. 0.321 0.222 0.899
## 9 CAGL0A00319g 1804. 0.322 0.152 0.583
## 10 CAGL0A00341g 654. 0.272 0.417 0.986
## # ℹ 5,114 more rowsDEGdf_up2x_FDR5_drugstrain = get_upregulated_genes(deseq_df_drugstrain)
DEGdf_down2x_FDR5_drugstrain = get_downregulated_genes(deseq_df_drugstrain)
print(DEGdf_up2x_FDR5_drugstrain, n = 20)## # A tibble: 9 × 5
## gene baseMean log2FC stderror padj
## <chr> <dbl> <dbl> <dbl> <dbl>
## 1 CAGL0J02530g 466. 2.07 0.376 0.0000599
## 2 CAGL0L06776g 1896. 1.37 0.274 0.000471
## 3 CAGL0I09856g 1624. 1.35 0.368 0.0246
## 4 CAGL0K04719g 2367. 1.29 0.348 0.0238
## 5 CAGL0M06347g 2086. 1.24 0.235 0.000134
## 6 CAGL0L08426g 1163. 1.23 0.331 0.0233
## 7 CAGL0K10824g 1318. 1.18 0.289 0.00899
## 8 CAGL0M08800g 1528. 1.18 0.327 0.0290
## 9 CAGL0M03839g 21921. 1.12 0.313 0.0325print(DEGdf_down2x_FDR5_drugstrain, n = 20)## # A tibble: 22 × 5
## gene baseMean log2FC stderror padj
## <chr> <dbl> <dbl> <dbl> <dbl>
## 1 CAGL0F06875g 11158. -2.81 0.398 0.00000000921
## 2 CAGL0J06402g 2664. -2.34 0.472 0.000508
## 3 CAGL0M01892g 39.9 -1.90 0.510 0.0233
## 4 CAGL0G02585g 8260. -1.79 0.385 0.00170
## 5 CAGL0F02431g 5599. -1.77 0.394 0.00288
## 6 CAGL0F04917g 114. -1.73 0.441 0.0151
## 7 CAGL0I09592g 938. -1.72 0.450 0.0203
## 8 CAGL0K07788g 14241. -1.67 0.431 0.0167
## 9 CAGL0C03872g 10721. -1.67 0.399 0.00763
## 10 CAGL0I08987g 949. -1.47 0.402 0.0253
## 11 CAGL0L02079g 7782. -1.47 0.322 0.00224
## 12 CAGL0K11616g 5367. -1.44 0.340 0.00697
## 13 CAGL0J09240g 9171. -1.44 0.354 0.0100
## 14 CAGL0E06688g 683. -1.37 0.341 0.0107
## 15 CAGL0C03443g 15756. -1.34 0.297 0.00275
## 16 CAGL0B01507g 734. -1.27 0.233 0.0000599
## 17 CAGL0G04807g 1090. -1.21 0.321 0.0222
## 18 CAGL0L01551g 1556. -1.18 0.287 0.00899
## 19 CAGL0I07711g 387. -1.16 0.285 0.0100
## 20 CAGL0G08668g 2336. -1.14 0.263 0.00538
## # ℹ 2 more rowsp_drugstrain = volcano_plot(deseq_df_drugstrain, DEGdf_up2x_FDR5_drugstrain, DEGdf_down2x_FDR5_drugstrain,
xlabel = "log2 fold-change\nmore, BG2 more, CBS138\n← →") +
ggtitle("Azole vs CT differences\nstrain BG2 vs CBS138")
p_drugstrain## Warning: Removed 10 rows containing missing values or values outside the scale range
## (`geom_point()`).
write.csv(deseq_df_drugstrain, "../data/DESeq2/DrugStrainInteractions/DrugStrain_CBS138_vs_BG2_allDESeq.csv")
write.csv(DEGdf_up2x_FDR5_drugstrain, "../data/DESeq2/DrugStrainInteractions/DrugStrain_CBS138_vs_BG2_up2x_FDR5.csv")
writeLines(DEGdf_up2x_FDR5_drugstrain$gene, "../data/DESeq2/DrugStrainInteractions/DrugStrain_CBS138_vs_BG2_up2x_FDR5_names.txt")
write.csv(DEGdf_down2x_FDR5_drugstrain, "../data/DESeq2/DrugStrainInteractions/DrugStrain_CBS138_vs_BG2_down2x_FDR5.csv")
writeLines(DEGdf_down2x_FDR5_drugstrain$gene, "../data/DESeq2/DrugStrainInteractions/DrugStrain_CBS138_vs_BG2_down2x_FDR5_names.txt")Volcano plot drug-strain interactions with highlighted genes
Highlighting calcium transporters MID1, ECM7, CCH1.
# Warning! This code chunk is based on manually reading in a file with gene names only of calculated deseq genes. It would be better to do a merge on all Cg gene names.
calcium_transporters <-
tribble(~gene, ~name,
"CAGL0B02211g", "CCH1",
"CAGL0M03597g", "MID1",
"CAGL0M00748g", "ECM7")
favourite_TFs <-
tribble(~gene, ~name,
"CAGL0M08800g", "YAP6",
"CAGL0L06776g", "GAT3/4")
drugstrain_down_names <-
read_tsv("../data/DESeq2/DrugStrainInteractions/DrugStrain_CBS138_vs_BG2_down2x_FDR5_fungidbtable.txt") %>%
select(gene, name) %>%
filter(!is.na(name))## Rows: 22 Columns: 3
## ── Column specification ────────────────────────────────────────────────────────
## Delimiter: "\t"
## chr (3): gene, description, name
##
## ℹ Use `spec()` to retrieve the full column specification for this data.
## ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.p_summary_volcanos_labels =
plot_grid(
p_cbd +
geom_label_repel(data = deseq_df_cbd %>%
right_join(calcium_transporters, by = "gene"),
aes(label = name),
min.segment.length = 0, max.overlaps = 20,
box.padding = 0.1, label.padding = 0.1),
p_drugnodrug_bc +
geom_label_repel(data = deseq_df_drugnodrug_bc %>%
right_join(calcium_transporters, by = "gene"),
aes(label = name),
min.segment.length = 0, max.overlaps = 20,
box.padding = 0.1, label.padding = 0.1),
p_drugstrain +
geom_label_repel(data = deseq_df_drugstrain %>%
right_join(
bind_rows(calcium_transporters,
favourite_TFs,
drugstrain_down_names),
by = "gene"),
aes(label = name),
min.segment.length = 0, max.overlaps = 20,
box.padding = 0.1, label.padding = 0.1),
ncol = 1, nrow = 3) +
scale_y_continuous("-log10(p)",
limits = c(0,5), expand = c(0,0),
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## Adding another scale for y, which will replace the existing scale.p_summary_volcanos_labels## Warning: ggrepel: 9 unlabeled data points (too many overlaps). Consider
## increasing max.overlaps
ggsave("../figures/summary_volcano_plots_genelabels.png",
plot = p_summary_volcanos_labels,
width = 7.5, height = 9)Venn Diagram of DEG lists
library(VennDiagram)## Loading required package: grid## Loading required package: futile.logger# Generate 3 sets of 200 words
set1 <- paste(rep("word_" , 200) , sample(c(1:1000) , 200 , replace=F) , sep="")
set2 <- paste(rep("word_" , 200) , sample(c(1:1000) , 200 , replace=F) , sep="")
set3 <- paste(rep("word_" , 200) , sample(c(1:1000) , 200 , replace=F) , sep="")
set.seed(20190708)
genes <- paste("gene",1:1000,sep="")
x <- list(
A = sample(genes,300),
B = sample(genes,525),
C = sample(genes,440),
D = sample(genes,350)
)
# Chart
venn.diagram(
x = list(set1, set2, set3),
category.names = c("Set 1" , "Set 2 " , "Set 3"),
filename = NULL,
output=TRUE
)## (polygon[GRID.polygon.15957], polygon[GRID.polygon.15958], polygon[GRID.polygon.15959], polygon[GRID.polygon.15960], polygon[GRID.polygon.15961], polygon[GRID.polygon.15962], text[GRID.text.15963], text[GRID.text.15964], text[GRID.text.15965], text[GRID.text.15966], text[GRID.text.15967], text[GRID.text.15968], text[GRID.text.15969], text[GRID.text.15970], text[GRID.text.15971], text[GRID.text.15972])display_venn <- function(x, ...){
library(VennDiagram)
grid.newpage()
venn_object <- venn.diagram(x, filename = NULL, ...)
grid.draw(venn_object)
}
display_venn(
x,
category.names = c("Set 1" , "Set 2 " , "Set 3", "Set 4"),
fill = c("#999999", "#E69F00", "#56B4E9", "#009E73")
)
display_venn(x)
library("ggVennDiagram")##
## Attaching package: 'ggVennDiagram'## The following object is masked from 'package:tidyr':
##
## uniteggVennDiagram(x, label_alpha = 0)
cf_up = as.vector(ortho_cb_c_up$gene)
cbd_up = as.vector(DEGdf_up2x_FDR5_cbd$gene)
cbf_up = as.vector(DEGdf_up2x_FDR5_cbf$gene)
bf_up = as.vector(ortho_cb_b_up$gene_id_cbs138)
y <- list(
CBS138_FLUC = cf_up,
strain_DMSO = cbd_up,
strain_FLUC = cbf_up,
BG2_FLUC = bf_up
)
display_venn(
y,
fill = c("#999999", "#E69F00", "#56B4E9", "#009E73")
)
print(head(DEGdf_up2x_FDR5_cbd))## # A tibble: 6 × 5
## gene baseMean log2FC stderror padj
## <chr> <dbl> <dbl> <dbl> <dbl>
## 1 CAGL0K00110g 13966. 12.5 0.809 3.70e- 51
## 2 CAGL0C00110g 4327. 10.3 0.274 1.58e-303
## 3 CAGL0H10626g 203. 9.79 0.873 4.30e- 27
## 4 CAGL0E00187g 550. 8.81 0.816 3.86e- 25
## 5 CAGL0E06666g 2836. 8.68 0.823 6.27e- 24
## 6 CAGL0K13024g 1275. 8.65 0.334 9.32e-145import pandas as pd
plt.rcParams['svg.fonttype'] = 'none'
rlog_all_p = r.rlog_all_df
rlog_all_p = rlog_all_p.reset_index().rename(columns={'index': 'Geneid'})
filamentous_genes = ["CAGL0H02145g", "CAGL0I01254g", "CAGL0I09856g", "CAGL0K04169g", "CAGL0M03663g", "CAGL0M09042g"]
cell_adhesion_genes = ["CAGL0K00110g", "CAGL0A01584g", "CAGL0I09856g", "CAGL0K12078g", "CAGL0I00220g", "CAGL0E06688g", "CAGL0C00110g"]
s = rlog_all_p[rlog_all_p["Geneid"].isin(cell_adhesion_genes)]
t = s.set_index("Geneid")
#plt.figure(figsize=(10, 10))
#plt.subplots_adjust(left=0.5, right=1.5, bottom=4.0)
g = sns.clustermap(t, cmap='vlag', method="single", annot_kws={"size": 7})
plt.setp(g.ax_heatmap.get_yticklabels(), rotation=0) # For y axis
plt.show()
#plt.savefig("/Users/s1964600/Work/random_figures/new_svg/cpac_scer_deg.svg")
plt.close()Composite figures
Figure 3 - Azole drugs induce a consistent transcriptomic response, overlaid on strain-dependent baseline gene expression.
- Principal Component Analysis shows that RNA-seq samples cluster by strain and by azole drug treatment. Principal components 1 and 2 of the regularized logarithm of counts per gene are shown for all samples; see methods for details.
- Between-sample variance is concentrated in principal components 1 and 2, that panel a shows cluster by strain and azole treatment.
- There are extensive baseline gene expression differences between strains BG2 and CBS138.
- A consistent azole-dependent transcriptomic response is identified by pooling azole-dependent differential expression across both FCZ and VCZ drugs across both strains BG2 and CBS138.
- There are minimal strain-dependent differences in drug-induced gene
expression, detected using the interaction term in a DESeq2 analysis
with both factors (
design = ~ Strain * Drug). See methods for details of differential gene expression analysis across 3 biological replicates using DESeq2, and supplementary figure SX for additional pairwise differential expression plots.
Load gene info
Load gene info from FungiDB with some of the important gene names.
CBS138_geneinfo <-
read_tsv("../data/genomes/CBS138_allgenes.txt",
col_names = c("Geneid", "Transcriptid","GenomicLocation", "Description", "Name"),
skip = 1,
na = c("", "NA", "N/A"))## Rows: 5615 Columns: 5
## ── Column specification ────────────────────────────────────────────────────────
## Delimiter: "\t"
## chr (5): Geneid, Transcriptid, GenomicLocation, Description, Name
##
## ℹ Use `spec()` to retrieve the full column specification for this data.
## ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.BG2_geneinfo <-
read_tsv("../data/genomes/BG2_allgenes.txt",
col_names = c("Geneid", "Transcriptid","GenomicLocation", "Description"),
skip = 1,
na = c("", "NA", "N/A")) %>%
mutate(Name = stringr::str_extract(Description, "^[A-Z]+[0-9]+"))## Rows: 5481 Columns: 4
## ── Column specification ────────────────────────────────────────────────────────
## Delimiter: "\t"
## chr (4): Geneid, Transcriptid, GenomicLocation, Description
##
## ℹ Use `spec()` to retrieve the full column specification for this data.
## ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.Plot groups of genes
Figure 4 - Azole drugs induce differential expression of specific genetic pathways.
The goal is to Visualise drug-dependent DGE across strains
First make a data frame of:
- deseq results drug vs no drug
- for both drugs separately
- in both strains separately
## # A tibble: 20,886 × 9
## gene_id_cbs138 gene_id_bg2 Strain Drug baseMean log2FC stderror padj
## <chr> <chr> <chr> <chr> <dbl> <dbl> <dbl> <dbl>
## 1 CAGL0A00165g GWK60_A00055 CBS138 FCZ 837. 0.320 0.174 0.126
## 2 CAGL0A00187g GWK60_A00077 CBS138 FCZ 1592. 0.293 0.179 0.179
## 3 CAGL0A00209g GWK60_A00099 CBS138 FCZ 6112. 0.0175 0.178 0.946
## 4 CAGL0A00231g GWK60_A00121 CBS138 FCZ 428. -0.698 0.308 0.0543
## 5 CAGL0A00253g GWK60_A00143 CBS138 FCZ 1941. 0.213 0.173 0.330
## 6 CAGL0A00275g GWK60_A00165 CBS138 FCZ 2638. -0.106 0.151 0.603
## 7 CAGL0A00297g GWK60_A00187 CBS138 FCZ 1434. 0.385 0.176 0.0642
## 8 CAGL0A00319g GWK60_A00209 CBS138 FCZ 1575. 0.557 0.178 0.00633
## 9 CAGL0A00341g GWK60_A00231 CBS138 FCZ 269. 1.26 0.317 0.000354
## 10 CAGL0A00363g GWK60_A00253 CBS138 FCZ 10119. -0.330 0.285 0.361
## # ℹ 20,876 more rows
## # ℹ 1 more variable: Strain_Drug <fct>Then load the genelist.
gene_list_5groups <-
read_excel("../data/gene_lists/Gene lists Ribeiro et al 2025.xlsx",
sheet = 2) %>%
mutate(Group = as_factor(Group),
gene_name = coalesce(gene_name, gene_id_cbs138) %>%
as_factor() %>% fct_rev() )
gene_list_5groups## # A tibble: 45 × 4
## Group gene_id_cbs138 gene_name notes
## <fct> <chr> <fct> <chr>
## 1 azole specific CAGL0A00451g PDR1 Multi-drug transporter
## 2 azole specific CAGL0M01760g CDR1 Multi-drug transporter
## 3 azole specific CAGL0F02717g PDH1 Multi-drug transporter, aka CDR2
## 4 azole specific CAGL0I04862g SNQ2 <NA>
## 5 azole specific CAGL0D05940g ERG1 <NA>
## 6 azole specific CAGL0L10714g ERG2 <NA>
## 7 azole specific CAGL0F01793g ERG3 <NA>
## 8 azole specific CAGL0M07656g ERG5 <NA>
## 9 azole specific CAGL0H04653g ERG6 <NA>
## 10 azole specific CAGL0J10824g ERG7 <NA>
## # ℹ 35 more rowsNow join the genelist to the deseq data frame.
deseq_4x_genelist <-
left_join(gene_list_5groups, deseq_df_4x,
by = "gene_id_cbs138",
) %>%
mutate(Strain_Drug = fct_relabel(Strain_Drug,
~ str_replace(., "_", ", ")))Next, Make a heatmap of DGE in all 4 conditions using facet_grid.
genelist_heatmap_pieces <- list(
geom_tile(aes(x = Strain_Drug, y = gene_name, fill = log2FC)),
scale_fill_gradient2(limits = c(-3,3), oob = scales::squish),
facet_grid(Group ~ ., drop = TRUE, scales = "free_y", space = "free_y"),
xlab("Strain, Drug"),
theme(axis.text.x = element_text(angle = 45, hjust = 1, vjust = 1),
axis.title.y = element_blank())
)
genelist_heatmap <-
ggplot(data = deseq_4x_genelist) +
genelist_heatmap_pieces
genelist_heatmap
ggsave("../figures/genelist_heatmap.svg",
genelist_heatmap,
height = 8, width = 3.4)This heatmap wwas then edited manually using inkscape, in
figures/genelist_heatmap_manualedit.svg.
Figure 4 legend
Azoles induce expression of select multidrug transporters (PDR1 transcription factor, CDR1 transporter, PDH1 transporter, but not the SNQ2 transporter), along with multiple ergosterol biosynthesis genes (ERG1, etc.). Azoles also induce expression of the yapsin family of aspartyl proteases (YPS1, etc.). Azoles further induce differential expression of different cell wall genes.
Azoles induce expression of multiple genes in the CRZ1 calcineurin-responsive transcription factor pathway, and other key stress response genes.